OTAR3088/CellFinder-all · Datasets at Hugging Face

sentences stringlengths 0 2.55k	entities listlengths 0 23	file_id stringclasses 10 values	ner listlengths 1 1
A positive score indicated a higher likelihood of being AS in both human and mouse.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "A", "positive", "score", "indicated", "a", "higher", "likel...
ACEScan was updated in the following ways.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "ACEScan", "was", "updated", "in", "the", "following", "ways", "." ] } ]
Firstly, instead of relying on orthology information by Ensembl, and then aligning flanking introns in “orthologous” exons, conserved exonic and intronic regions in human and mouse from genome-wide multiple alignments were extracted.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Secondly, whereas in our previous analysis exons from the longest transcript in Ensembl were utilized, now we collapsed all the transcripts available at the UCSC genome browser and analyzed all exons in the entire gene loci.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
ACEScan was utilized to assign ACEScan scores to all ∼162,000 internal exons in our genes.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "ACEScan", "was", "utilized", "to", "assign", "ACEScan", "sc...
Exons annotated as first or last exons in Refseq mRNAs were excluded from our analysis, resulting in 4,487 positive-scoring exons, 2-fold more exons than originally published.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Here we repeated our analysis with exons with positive ACEScan scores (ACE[+]) instead of EST-SEs.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Here", "we", "repeated", "our", "analy...
If we required that none of the points per probeset (exon) was significant, 2% (1,645 of 71,731) of exons (after probeset mapping) were ACE[+] (Figure 6B).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Shuffling the mapping between these probesets and exons resulted in 3% (2,044 of 71,731) of exons being ACE[+] (Figure 6B).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...
These percentages were not significantly different from the 2.7% observed from all exons (4,487 of the 162,000 exons that were scored by ACEScan).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...
By raising the requirement that probesets had to contain five significant points, the percentage of ACE[+] exons increased from 4% to 11%.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...
However, the sample sizes were small.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "However", ",", "the", "sample", "sizes", "were", "small", "." ] } ]
In comparison, the shuffled probesets at the same requirements remained at ∼4%.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "comparison", ",", "the", "shuffled", "probesets", "at", "t...
Similar overall trends were observed with hCNS-SCns versus HUES6-ES and the derived NPs versus hESCs (Figure 6B).	[ { "end": 49, "label": "CellType", "start": 42 }, { "end": 100, "label": "CellType", "start": 95 }, { "end": 87, "label": "CellType", "start": 84 }, { "end": 67, "label": "CellLine", "start": 59 }, { "end": 51, "label": "CellType", "start": ...	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "B-CellType", "O", "B-CellLine", "O", "O", "O", "B-CellType", "O", "B-CellType", "O", "O", "O", "O", "O" ], "tokens": [ "Similar", ...
In total, 7.5% (131 of 1,737) of REAP [+] exons were designated as ACEScan[+] compared to 2.4% (2,328 of 97,437) of REAP[−] exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
This result suggested that a small but significantly enriched fraction of AS events in hESCs versus NPs was likely to be evolutionarily conserved in human and mouse.	[ { "end": 103, "label": "CellType", "start": 100 }, { "end": 92, "label": "CellType", "start": 87 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "...
In conclusion, our results suggested that REAP predictions were congruent with predictions from two independent, orthogonal methods.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "conclusion", ",", "our", ...
Experimental Validation of Alternative ExonsThe sensitivity and specificity of REAP in the identification of REAP[+] exons was tested by RT-PCR.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Experimental", "Validat...
To validate REAP[+] alternative exons, RT-PCR primers were designed in the flanking exons to amplify both isoforms.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "To", "validate", "REAP[+", "]", ...
To be a positively validated candidate, the PCR products on a gel had to satisfy all of the following criteria: (i) at least one isoform with the expected size must be visible in each cell type; (ii) the relative abundance of the two isoforms must be altered between two cell types and the direction of change have to be...	[ { "end": 427, "label": "CellType", "start": 422 }, { "end": 447, "label": "CellType", "start": 444 }, { "end": 517, "label": "CellType", "start": 512 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
For simplicity of design, we tested candidates predicted from Cyt-ES versus hCNS-SCns.	[ { "end": 85, "label": "CellType", "start": 76 }, { "end": 68, "label": "CellLine", "start": 62 }, { "end": 83, "label": "CellType", "start": 76 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellLine", "O", "B-CellType", "O" ], "tokens": [ "For", "simplicity", "of", "design", ",", "we", "tested", ...
Fifteen REAP[+] exons with at least two significant outliers (out of five) were randomly chosen as predicted alternative events and thirty-five exons with less than two significant outliers were randomly chosen as constitutive events (Table S3).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Nine of the fifteen exons (60%) were validated as AS events by our criteria.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Nine", "of", "the", "fifteen", "exons", "("...
The sensitivity and specificity of the algorithm at the cutoff of two is 69% and 77%.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "sensitivity", "and", "specificity", ...
Increasing the cutoff to three increased the specificity to 85%, with a slight decrease in sensitivity to 67% (Figure 7A).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...
The patterns of AS in hESCs were similar in both Cyt-ES and HUES6-ES for all AS events validated, but the NPs (Cyt-NP, HUES6-NP, and hCNS-SCns) had more varied AS.	[ { "end": 55, "label": "CellLine", "start": 49 }, { "end": 140, "label": "CellType", "start": 133 }, { "end": 124, "label": "CellLine", "start": 119 }, { "end": 68, "label": "CellLine", "start": 60 }, { "end": 142, "label": "CellType", "star...	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellLine", "O", "B-CellLine", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O"...
The pattern of AS in the REAP[+] exons in the SLK (serine/threonine kinase 2) and POT1 (protection of telomeres 1) genes showed remarkable agreement within derived NPs and hCNS-SCns (Figure 7B).	[ { "end": 179, "label": "CellType", "start": 172 }, { "end": 167, "label": "CellType", "start": 164 }, { "end": 181, "label": "CellType", "start": 172 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
The AS exon in SLK was observed to be included in hESCs and completely excluded in NPs; the AS exon in the POT1 gene was included more in hESCs and a smaller isoform persisted in NPs.	[ { "end": 86, "label": "CellType", "start": 83 }, { "end": 55, "label": "CellType", "start": 50 }, { "end": 143, "label": "CellType", "start": 138 }, { "end": 182, "label": "CellType", "start": 179 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "...
The AS patterns of the other verified REAP[+] exons were consistently similar in hESCs but were more varied in the NP.	[ { "end": 86, "label": "CellType", "start": 81 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", ...
Interestingly, the patterns of AS in the derived NPs (Cyt-NP and HUES6-NP) were not always identical to those of hCNS-SCns.	[ { "end": 70, "label": "CellLine", "start": 65 }, { "end": 122, "label": "CellType", "start": 113 }, { "end": 52, "label": "CellType", "start": 49 }, { "end": 120, "label": "CellType", "start": 113 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O" ], "tokens"...
For example, the AS exon in the EHBP1 (EH domain binding protein 1) gene was included in hESCs but skipped in hCNS-SCns, and both isoforms were present in the derived NPs (Figure 7B).	[ { "end": 117, "label": "CellType", "start": 110 }, { "end": 94, "label": "CellType", "start": 89 }, { "end": 119, "label": "CellType", "start": 110 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "B-CellType", "...
As another example, the AS exon in the SORBS1 (sorbin and SH3 domain containing 1) gene was skipped in hESCs and included in hCNS-SCns, but exhibited an intermediate pattern in the derived NPs.	[ { "end": 192, "label": "CellType", "start": 189 }, { "end": 108, "label": "CellType", "start": 103 }, { "end": 134, "label": "CellType", "start": 125 }, { "end": 132, "label": "CellType", "start": 125 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", ...
However, in some cases, the AS patterns in the derived NPs were different from both hESCs and hCNS-SCns (such as in the AS exon in UNC84A, SIRT1, and MLLT10).Figure 7RT-PCR Validation of REAP-Predicted Alternative Exons(A) Probesets (exons) were considered REAP[+] candidates if they contained at least N = 2 (white bars...	[ { "end": 58, "label": "CellType", "start": 55 }, { "end": 103, "label": "CellType", "start": 94 }, { "end": 89, "label": "CellType", "start": 84 }, { "end": 101, "label": "CellType", "start": 94 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "B-CellType", "O", "B-CellType", "O", "O", "O", "O", "O"...
True positive (TP), true negative (TN), false positive (FP), and false negative (FN) rates were calculated from RT-PCR-validated REAP[+] exons at the different cutoffs (N = 2, 3, 4).(B) Nine RT-PCR validated REAP[+] AS events in hESCs (Cyt-ES and HUES6-ES), derived NPs (Cyt-NP and HUES6-NP), and hCNS-SCns.	[ { "end": 255, "label": "CellLine", "start": 247 }, { "end": 242, "label": "CellLine", "start": 236 }, { "end": 234, "label": "CellType", "start": 229 }, { "end": 306, "label": "CellType", "start": 297 }, { "end": 269, "label": "CellType", "...	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Arrows indicate the larger (exon-included) isoforms and smaller (exon-skipped) isoforms.(C) RT-PCR of REAP[+] alternative exons from EHBP1, SLK, and RAI14 across a panel of human tissues.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Arrows indicate the larger (exon-included) isoforms and smaller (exon-skipped) isoforms.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Arrows", "indicate", "the", "larger", "(", "exon-included", ")", ...
First, given three independent samples each from two conditions, we concluded that REAP was able to identify AS events with high specificity but with moderate sensitivity.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Second, AS events in hESCs were more similar, whereas the AS events in derived NPs were consistent with or intermediate to the benchmark hCNS-SCns, likely reflecting differences in the cell lines and/or differentiation protocols.	[ { "end": 82, "label": "CellType", "start": 79 }, { "end": 26, "label": "CellType", "start": 21 }, { "end": 146, "label": "CellType", "start": 137 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "...
In addition, we tested the AS patterns of REAP[+] exons from EHBP1, SLK, and RAI14 in a panel of differentiated human tissues (Figure 7C).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
The REAP[+] alternative exon in the RAI14 (retinoic acid induced 14) gene was observed to have the same AS pattern in NPs as in frontal and temporal cortex and in several other, non-brain adult tissues, such as heart and spleen.	[ { "end": 227, "label": "Tissue", "start": 221 }, { "end": 216, "label": "Tissue", "start": 211 }, { "end": 155, "label": "Tissue", "start": 140 }, { "end": 135, "label": "Tissue", "start": 128 }, { "end": 121, "label": "CellType", "start": ...	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", ...
The AS pattern of the REAP[+] exon in the SLK gene in NPs was similar to most differentiated tissues; however, the relatively strong inclusion of the exon in hESCs was unique.	[ { "end": 163, "label": "CellType", "start": 158 }, { "end": 57, "label": "CellType", "start": 54 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Even in esophagus, kidney, liver, and prostate, both isoforms were present.	[ { "end": 32, "label": "Tissue", "start": 27 }, { "end": 25, "label": "Tissue", "start": 19 }, { "end": 17, "label": "Tissue", "start": 8 }, { "end": 46, "label": "Tissue", "start": 38 } ]	17967047	[ { "tags": [ "O", "O", "B-Tissue", "O", "B-Tissue", "O", "B-Tissue", "O", "O", "B-Tissue", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Even", "in", "esophagus", ",", "kidney", ...
The relative ratio of the exon-included to exon-skipped isoforms in SLK likely represents an ESC-specific AS signature.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "relative", "ratio", "of", "the", "ex...
The alternative exon in the EHBP1 gene was unusual.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "alternative", "exon", "in", "the", "EHBP1", "gene", "was", "unusual", "." ] } ]
The exon was included in hESCs but also in frontal cortex and temporal cortex, a finding that was unexpected given the exclusion of the exon in hCNS-SCns (Figure 7C).	[ { "end": 57, "label": "Tissue", "start": 43 }, { "end": 153, "label": "CellType", "start": 144 }, { "end": 77, "label": "Tissue", "start": 62 }, { "end": 30, "label": "CellType", "start": 25 }, { "end": 151, "label": "CellType", "start": 14...	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "B-Tissue", "I-Tissue", "O", "B-Tissue", "I-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O",...
The AS pattern in hCNS-SCns may represent a transient, early neuronal molecular change.	[ { "end": 27, "label": "CellType", "start": 18 }, { "end": 69, "label": "Tissue", "start": 61 }, { "end": 25, "label": "CellType", "start": 18 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "B-Tissue", "O", "O", "O" ], "tokens": [ "The", "AS", "pattern", "in", "hCNS-SCns", "may", "repr...
Functional and Expression Characteristics of REAP[+] GenesIn total, 1,500 genes were identified that contained 1,737 REAP[+] exons, 68% of which lacked prior transcript (EST/cDNA) evidence for AS.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
To determine whether genes that contained REAP[+] exons, which we refer to as REAP[+] genes, are biased toward particular biological activities, REAP[+] genes were compared to a set of REAP analyzed genes not found to have REAP[+] exons (REAP[−] genes).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
A Gene Ontology analysis revealed that REAP[+] genes are enriched for GO molecular function categories “ATP binding,” “helicase activity,” “protein serine/theronine kinase activity,” “small GTPase regulatory/interacting protein activity,” and “thyroid hormone receptor binding” (Table 1).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
In terms of GO biological process categories, REAP[+] genes were more frequently involved in “ubiquitin cycle.”	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "terms", "of", "G...
Similar results were obtained when we compared REAP[+] genes to all human genes that did not contain REAP[+] exons (Table 1) [55].Table 1Significantly Enriched Gene Ontology Terms in REAP[+] Genes (Cutoff of Two Significant “Outliers” per Probeset)Next we asked if REAP[+] genes are differentially expressed in hESCs com...	[ { "end": 332, "label": "CellType", "start": 329 }, { "end": 316, "label": "CellType", "start": 311 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
For this analysis, the t-statistics computed above measuring the enrichment of a gene in hESCs relative to NPs was utilized for only REAP-analyzed genes.	[ { "end": 110, "label": "CellType", "start": 107 }, { "end": 94, "label": "CellType", "start": 89 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "...
At a defined absolute-valued cutoff, genes were divided into three categories: “enriched in hESCs,” “enriched in NP,” or “unchanged” (Figure 8A).	[ { "end": 97, "label": "CellType", "start": 92 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Increasing the t-statistic cutoff from one to five, the fraction of REAP[+] genes relative to REAP-analyzed genes remained constant in the “unchanged” categories (Figure 8B).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
However, the fraction of REAP[+] exons decreased significantly in “enriched in hESCs” and “enriched in NPs” categories.	[ { "end": 106, "label": "CellType", "start": 103 }, { "end": 84, "label": "CellType", "start": 79 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O" ], "tokens"...
If we increased the cutoffs on genes that were randomly assigned as REAP[+] and REAP[−], controlling for the same number of genes in each category, we observed that the fraction of REAP[+] exons remained unchanged for all three categories (Figure 8C).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
To illustrate, at a cutoff of five, 10% (29 of 267) of enriched NP genes were REAP[+] genes and 8.8% (102 of 1,162) of enriched hESC genes were REAP[+], significantly different (p < 0.000005) from the random control where ∼14% of enriched NP and enriched hESC genes were REAP[+].	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
At a cutoff of five, 14% (1,368 of 9,636) of genes that were expressed at similar levels between hESCs and NPs were REAP[+].	[ { "end": 110, "label": "CellType", "start": 107 }, { "end": 102, "label": "CellType", "start": 97 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "B-CellType", "...
Our results suggested that a strategy of focusing on differentially expressed genes would miss at least 14% of transcriptionally unchanged genes that may nevertheless have functional AS differences between hESCs and NPs.	[ { "end": 211, "label": "CellType", "start": 206 }, { "end": 219, "label": "CellType", "start": 216 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Figure 8Analysis of REAP[+] Genes Relative to Transcriptional Differences(A) Histogam of t-statistics computed from gene-level signal estimates measuring the enrichment of genes in hESC and in NP.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Genes on the right of the vertical line at 5 were designated enriched in hESC and genes on the left of the vertical line at −5 were designated enriched in NP; genes in between −5 and 5 were designated as “unchanged” or expressed similarly in hESC and NP.(B) Vertical bars representing the percentage of REAP[+] genes out...	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Similar representation as in (B).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Similar", "representation", "as", "in", "(", "B", ")", "." ] } ]
Conserved Intronic Splicing Regulatory Elements Proximal to REAP[+] hESC and NP ExonsMany, if not most, alternative exons undergo cell type–specific regulation by the binding of trans-factors to splicing regulatory cis-elements located proximal to or within the exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
As many tissue-specific splicing cis-regulatory elements were localized in intronic regions of AS exons, we focused on the identification of intronic splicing regulatory elements (ISREs) proximal to REAP[+] exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
In addition, we wanted to identify both common and cell type–specific ISREs.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "addition", ",", "we", "wanted", "to", "identify", ...
Three sets of exons were generated: (i) REAP[+] exons that were predicted to be included in NPs and skipped in hESCs (REAP[+]NP); (ii) REAP[+] exons that were predicted to be included in hESCs and skipped in NPs (REAP[+]hESC); and (iii) all REAP[−] exons.	[ { "end": 95, "label": "CellType", "start": 92 }, { "end": 116, "label": "CellType", "start": 111 }, { "end": 211, "label": "CellType", "start": 208 }, { "end": 192, "label": "CellType", "start": 187 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "B-CellType", "...
Regions of 400 base pairs flanking the exons were targeted for search.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Regions", "of", "400", "base", "pairs", "flanking", "the", "exons", "were", ...
Initially, 5-mers that were significantly enriched between the upstream and downstream intronic regions of REAP[+]NP and REAP[+]ES relative to REAP[−] exons were enumerated.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...
We were not able to identify 5-mers that were statistically significantly different.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "We", "were", "not", "able", "to", "identify", "5-mers", "that", "were", "s...
Next, we focused on splicing signals that were conserved across mammalian genomes as a way of enhancing the signal of detecting functional splicing regulatory sequences [66].	[ { "end": 73, "label": "Tissue", "start": 64 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "...
Exons that were orthologous across human, dog, rat, and mouse were obtained and the flanking intronic regions were aligned (400 bases upstream and downstream separately; Figure 9A).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
We enumerated k-mers that were perfectly conserved across all four genomes in the upstream (and downstream) intronic regions.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "We", "enumerated", "k-mers",...
Each conserved k-mer was attributed a χ score representing its enrichment in a set of exons relative to another set of exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Each", "cons...
The higher the score, the more frequent the conserved k-mer was in the first set relative to the second set.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "higher", "...
As a negative control, the associations between REAP scores and exons were shuffled.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "As", "a", "negative", "control", ",", "the", "associations", "be...
The enrichment scores for all downstream intronic 5-mers for shuffled REAP[+]NP versus set REAP[−] exons (x-axis), and for shuffled REAP[+]ES exons versus REAP[−] exons (y-axis) were displayed (Figure 9B).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
At a χ cutoff of three, which corresponded to a p-value of 0.0015, the majority of 5-mers were not significantly enriched in either shuffled set.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Confident that no association of k-mers with shuffled REAP exons were found; we repeated the analyses for upstream and downstream intronic 5-mers for the original unshuffled sets.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
We identified 68 conserved 5-mers enriched upstream of REAP[+]NP exons; and 34 5-mers enriched upstream of REAP[+]ES exons (Figure 9C; Table S4).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...
Of the 5-mers that were significantly enriched upstream of REAP[+]NP exons, we identified a U-rich motif (UUUUU), a GU-rich motif (GUGUG), and a CU-rich motif (CCUCU, CUCUC, UCUCU, GCUCU).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
It is known that the heterogeneous ribonucleoprotein C (hnRNP C) binding site obtained by SELEX is five “U”s [67].	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ ...
GU-rich sequences in flanking intronic regions were shown to bind to splicing factor ETR-3 to regulate AS [68].	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "GU-rich", "sequences", "in",...
CU-rich sequences were shown to bind the splicing factor PTB [69].	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "CU-rich", "sequences", "were", "shown", "to", "bind", "the", "splicing", ...
Of the 5-mers enriched upstream of REAP[+]ES exons, we observed CUAAC, which resembled the splicing branch-signal.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Of", "the", "5-mers", "enriched", "ups...
Of the six 5-mers that were enriched upstream of both REAP[+]NP and REAP[+]ES exons, we identified GCAUG, which was previously shown to be an intronic splicing cis-element for the mammalian fibronectin and calcitonin/CGRP genes [70–72].	[ { "end": 189, "label": "Tissue", "start": 180 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
More recently, both mammalian Fox1 and 2 have been demonstrated to regulate alternatively spliced exons via UGCAUG binding sites in neighboring introns in neuronal cell cultures [73].Figure 9Conserved Intronic cis-Elements Enriched Proximal to REAP[+] Alternative Exons(A) Schematic describing the enumeration of introni...	[ { "end": 369, "label": "Tissue", "start": 360 }, { "end": 163, "label": "Tissue", "start": 155 }, { "end": 29, "label": "Tissue", "start": 20 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "B-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-Tissue", "O", ...
Red and green horizontal bars represent conserved intronic elements and nonconserved elements, respectively.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Red", "and", "green", "horizontal", "bars", "represent", "conserved", ...
Internal exons were divided into REAP[+]NP, REAP[+]ES, and REAP[−] exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Internal", "exons", "were", "divided", "into", "REAP[+]NP", ",", "REAP[+]ES...
The χ statistic was computed to represent the enrichment of conserved elements in intronic regions flanking REAP[+]NP versus REAP[−] exons (x-axis), and REAP[+]ES versus REAP[−] exons (y-axis).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
The sign represented the direction of change, i.e., positive if enriched in introns flanking REAP[+] versus REAP[−] exon.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "sign"...
Each conserved 5-mer was associated with two numbers: the enrichment in introns proximal to REAP[+]NP versus REAP[−] exons (x-axis), and REAP[+]ES versus REAP[−] exons (y-axis).(B) Downstream intronic regions, where the association between REAP[+] designation and the exons was shuffled.(C) Upstream intronic regions.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Circled 5-mers in the upper right quadrant represent conserved 5-mers enriched in the upstream intronic regions of REAP[+]NP and REAP[+]ES exons.(D) Downstream intronic regions.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...
Circled 5-mers in the upper right quadrant represent conserved 5-mers enriched in the downstream intronic regions of REAP[+]NP and REAP[+]ES exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Circled", "5-mers", ...
Eighteen conserved 5-mers were significantly enriched in the downstream introns of REAP[+]ES exons; and 76 5-mers were enriched downstream of REAP[+]NP exons (Table S4, Figure 9D).	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
We identified a motif CUCAU resembling the Nova binding site YCAY [74], and a G-rich motif (AGGGG, GGGGA, GGGGC, GGGGG, GGGGU) enriched in the introns downstream of REAP[+]ES exons.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
G-rich motifs had previously been shown to be part of a bipartite signal that silences AS exons [75].	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "G-rich", "motifs", "had", ...
Of the five 5-mers that were enriched downstream of both REAP[+]NP and REAP[+]ES exons, GCAUG and a U-rich motif (UUUUU) were identified.	[]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...
We concluded that potential ISREs were enriched proximal to a subset of REAP[+] exons; in particular, the Fox1/2 binding site GCUAG may play a regulatory role in controlling AS events in hESCs and NPs.	[ { "end": 200, "label": "CellType", "start": 197 }, { "end": 192, "label": "CellType", "start": 187 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
The ability of ESCs to generate all three embryonic germ layers has raised the exciting possibility that hESCs may become an unlimited source of cells for transplantation therapies involving organs or tissues such as the liver, pancreas, blood, and nervous system, and become tools to explore the molecular mechanisms of...	[ { "end": 244, "label": "Tissue", "start": 239 }, { "end": 237, "label": "Tissue", "start": 229 }, { "end": 111, "label": "CellType", "start": 106 }, { "end": 264, "label": "Tissue", "start": 250 }, { "end": 20, "label": "CellType", "start":...	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "I-Tissue", "I-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...
Despite such interests, relatively little is understood about the molecular mechanisms defining their pluripotency and the molecular changes important for hESCs to differentiate into specific cell types.	[ { "end": 160, "label": "CellType", "start": 155 } ]	17967047	[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", ...

A positive score indicated a higher likelihood of being AS in both human and mouse.

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17967047

[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "A", "positive", "score", "indicated", "a", "higher", "likel...

ACEScan was updated in the following ways.

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17967047

[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "ACEScan", "was", "updated", "in", "the", "following", "ways", "." ] } ]

Firstly, instead of relying on orthology information by Ensembl, and then aligning flanking introns in “orthologous” exons, conserved exonic and intronic regions in human and mouse from genome-wide multiple alignments were extracted.

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17967047

[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Secondly, whereas in our previous analysis exons from the longest transcript in Ensembl were utilized, now we collapsed all the transcripts available at the UCSC genome browser and analyzed all exons in the entire gene loci.

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17967047

[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

ACEScan was utilized to assign ACEScan scores to all ∼162,000 internal exons in our genes.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "ACEScan", "was", "utilized", "to", "assign", "ACEScan", "sc...

Exons annotated as first or last exons in Refseq mRNAs were excluded from our analysis, resulting in 4,487 positive-scoring exons, 2-fold more exons than originally published.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Here we repeated our analysis with exons with positive ACEScan scores (ACE[+]) instead of EST-SEs.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Here", "we", "repeated", "our", "analy...

If we required that none of the points per probeset (exon) was significant, 2% (1,645 of 71,731) of exons (after probeset mapping) were ACE[+] (Figure 6B).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Shuffling the mapping between these probesets and exons resulted in 3% (2,044 of 71,731) of exons being ACE[+] (Figure 6B).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...

These percentages were not significantly different from the 2.7% observed from all exons (4,487 of the 162,000 exons that were scored by ACEScan).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...

By raising the requirement that probesets had to contain five significant points, the percentage of ACE[+] exons increased from 4% to 11%.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...

However, the sample sizes were small.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "However", ",", "the", "sample", "sizes", "were", "small", "." ] } ]

In comparison, the shuffled probesets at the same requirements remained at ∼4%.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "comparison", ",", "the", "shuffled", "probesets", "at", "t...

Similar overall trends were observed with hCNS-SCns versus HUES6-ES and the derived NPs versus hESCs (Figure 6B).

[ { "end": 49, "label": "CellType", "start": 42 }, { "end": 100, "label": "CellType", "start": 95 }, { "end": 87, "label": "CellType", "start": 84 }, { "end": 67, "label": "CellLine", "start": 59 }, { "end": 51, "label": "CellType", "start": ...

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "B-CellType", "O", "B-CellLine", "O", "O", "O", "B-CellType", "O", "B-CellType", "O", "O", "O", "O", "O" ], "tokens": [ "Similar", ...

In total, 7.5% (131 of 1,737) of REAP [+] exons were designated as ACEScan[+] compared to 2.4% (2,328 of 97,437) of REAP[−] exons.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

This result suggested that a small but significantly enriched fraction of AS events in hESCs versus NPs was likely to be evolutionarily conserved in human and mouse.

[ { "end": 103, "label": "CellType", "start": 100 }, { "end": 92, "label": "CellType", "start": 87 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "...

In conclusion, our results suggested that REAP predictions were congruent with predictions from two independent, orthogonal methods.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "conclusion", ",", "our", ...

Experimental Validation of Alternative ExonsThe sensitivity and specificity of REAP in the identification of REAP[+] exons was tested by RT-PCR.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Experimental", "Validat...

To validate REAP[+] alternative exons, RT-PCR primers were designed in the flanking exons to amplify both isoforms.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "To", "validate", "REAP[+", "]", ...

To be a positively validated candidate, the PCR products on a gel had to satisfy all of the following criteria: (i) at least one isoform with the expected size must be visible in each cell type; (ii) the relative abundance of the two isoforms must be altered between two cell types and the direction of change have to be...

[ { "end": 427, "label": "CellType", "start": 422 }, { "end": 447, "label": "CellType", "start": 444 }, { "end": 517, "label": "CellType", "start": 512 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

For simplicity of design, we tested candidates predicted from Cyt-ES versus hCNS-SCns.

[ { "end": 85, "label": "CellType", "start": 76 }, { "end": 68, "label": "CellLine", "start": 62 }, { "end": 83, "label": "CellType", "start": 76 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellLine", "O", "B-CellType", "O" ], "tokens": [ "For", "simplicity", "of", "design", ",", "we", "tested", ...

Fifteen REAP[+] exons with at least two significant outliers (out of five) were randomly chosen as predicted alternative events and thirty-five exons with less than two significant outliers were randomly chosen as constitutive events (Table S3).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Nine of the fifteen exons (60%) were validated as AS events by our criteria.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Nine", "of", "the", "fifteen", "exons", "("...

The sensitivity and specificity of the algorithm at the cutoff of two is 69% and 77%.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "sensitivity", "and", "specificity", ...

Increasing the cutoff to three increased the specificity to 85%, with a slight decrease in sensitivity to 67% (Figure 7A).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...

The patterns of AS in hESCs were similar in both Cyt-ES and HUES6-ES for all AS events validated, but the NPs (Cyt-NP, HUES6-NP, and hCNS-SCns) had more varied AS.

[ { "end": 55, "label": "CellLine", "start": 49 }, { "end": 140, "label": "CellType", "start": 133 }, { "end": 124, "label": "CellLine", "start": 119 }, { "end": 68, "label": "CellLine", "start": 60 }, { "end": 142, "label": "CellType", "star...

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellLine", "O", "B-CellLine", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O"...

The pattern of AS in the REAP[+] exons in the SLK (serine/threonine kinase 2) and POT1 (protection of telomeres 1) genes showed remarkable agreement within derived NPs and hCNS-SCns (Figure 7B).

[ { "end": 179, "label": "CellType", "start": 172 }, { "end": 167, "label": "CellType", "start": 164 }, { "end": 181, "label": "CellType", "start": 172 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

The AS exon in SLK was observed to be included in hESCs and completely excluded in NPs; the AS exon in the POT1 gene was included more in hESCs and a smaller isoform persisted in NPs.

[ { "end": 86, "label": "CellType", "start": 83 }, { "end": 55, "label": "CellType", "start": 50 }, { "end": 143, "label": "CellType", "start": 138 }, { "end": 182, "label": "CellType", "start": 179 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "...

The AS patterns of the other verified REAP[+] exons were consistently similar in hESCs but were more varied in the NP.

[ { "end": 86, "label": "CellType", "start": 81 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", ...

Interestingly, the patterns of AS in the derived NPs (Cyt-NP and HUES6-NP) were not always identical to those of hCNS-SCns.

[ { "end": 70, "label": "CellLine", "start": 65 }, { "end": 122, "label": "CellType", "start": 113 }, { "end": 52, "label": "CellType", "start": 49 }, { "end": 120, "label": "CellType", "start": 113 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O" ], "tokens"...

For example, the AS exon in the EHBP1 (EH domain binding protein 1) gene was included in hESCs but skipped in hCNS-SCns, and both isoforms were present in the derived NPs (Figure 7B).

[ { "end": 117, "label": "CellType", "start": 110 }, { "end": 94, "label": "CellType", "start": 89 }, { "end": 119, "label": "CellType", "start": 110 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "B-CellType", "...

As another example, the AS exon in the SORBS1 (sorbin and SH3 domain containing 1) gene was skipped in hESCs and included in hCNS-SCns, but exhibited an intermediate pattern in the derived NPs.

[ { "end": 192, "label": "CellType", "start": 189 }, { "end": 108, "label": "CellType", "start": 103 }, { "end": 134, "label": "CellType", "start": 125 }, { "end": 132, "label": "CellType", "start": 125 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", ...

However, in some cases, the AS patterns in the derived NPs were different from both hESCs and hCNS-SCns (such as in the AS exon in UNC84A, SIRT1, and MLLT10).Figure 7RT-PCR Validation of REAP-Predicted Alternative Exons(A) Probesets (exons) were considered REAP[+] candidates if they contained at least N = 2 (white bars...

[ { "end": 58, "label": "CellType", "start": 55 }, { "end": 103, "label": "CellType", "start": 94 }, { "end": 89, "label": "CellType", "start": 84 }, { "end": 101, "label": "CellType", "start": 94 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "B-CellType", "O", "B-CellType", "O", "O", "O", "O", "O"...

True positive (TP), true negative (TN), false positive (FP), and false negative (FN) rates were calculated from RT-PCR-validated REAP[+] exons at the different cutoffs (N = 2, 3, 4).(B) Nine RT-PCR validated REAP[+] AS events in hESCs (Cyt-ES and HUES6-ES), derived NPs (Cyt-NP and HUES6-NP), and hCNS-SCns.

[ { "end": 255, "label": "CellLine", "start": 247 }, { "end": 242, "label": "CellLine", "start": 236 }, { "end": 234, "label": "CellType", "start": 229 }, { "end": 306, "label": "CellType", "start": 297 }, { "end": 269, "label": "CellType", "...

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Arrows indicate the larger (exon-included) isoforms and smaller (exon-skipped) isoforms.(C) RT-PCR of REAP[+] alternative exons from EHBP1, SLK, and RAI14 across a panel of human tissues.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Arrows indicate the larger (exon-included) isoforms and smaller (exon-skipped) isoforms.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Arrows", "indicate", "the", "larger", "(", "exon-included", ")", ...

First, given three independent samples each from two conditions, we concluded that REAP was able to identify AS events with high specificity but with moderate sensitivity.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Second, AS events in hESCs were more similar, whereas the AS events in derived NPs were consistent with or intermediate to the benchmark hCNS-SCns, likely reflecting differences in the cell lines and/or differentiation protocols.

[ { "end": 82, "label": "CellType", "start": 79 }, { "end": 26, "label": "CellType", "start": 21 }, { "end": 146, "label": "CellType", "start": 137 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "...

In addition, we tested the AS patterns of REAP[+] exons from EHBP1, SLK, and RAI14 in a panel of differentiated human tissues (Figure 7C).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

The REAP[+] alternative exon in the RAI14 (retinoic acid induced 14) gene was observed to have the same AS pattern in NPs as in frontal and temporal cortex and in several other, non-brain adult tissues, such as heart and spleen.

[ { "end": 227, "label": "Tissue", "start": 221 }, { "end": 216, "label": "Tissue", "start": 211 }, { "end": 155, "label": "Tissue", "start": 140 }, { "end": 135, "label": "Tissue", "start": 128 }, { "end": 121, "label": "CellType", "start": ...

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", ...

The AS pattern of the REAP[+] exon in the SLK gene in NPs was similar to most differentiated tissues; however, the relatively strong inclusion of the exon in hESCs was unique.

[ { "end": 163, "label": "CellType", "start": 158 }, { "end": 57, "label": "CellType", "start": 54 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Even in esophagus, kidney, liver, and prostate, both isoforms were present.

[ { "end": 32, "label": "Tissue", "start": 27 }, { "end": 25, "label": "Tissue", "start": 19 }, { "end": 17, "label": "Tissue", "start": 8 }, { "end": 46, "label": "Tissue", "start": 38 } ]

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[ { "tags": [ "O", "O", "B-Tissue", "O", "B-Tissue", "O", "B-Tissue", "O", "O", "B-Tissue", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Even", "in", "esophagus", ",", "kidney", ...

The relative ratio of the exon-included to exon-skipped isoforms in SLK likely represents an ESC-specific AS signature.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "relative", "ratio", "of", "the", "ex...

The alternative exon in the EHBP1 gene was unusual.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "alternative", "exon", "in", "the", "EHBP1", "gene", "was", "unusual", "." ] } ]

The exon was included in hESCs but also in frontal cortex and temporal cortex, a finding that was unexpected given the exclusion of the exon in hCNS-SCns (Figure 7C).

[ { "end": 57, "label": "Tissue", "start": 43 }, { "end": 153, "label": "CellType", "start": 144 }, { "end": 77, "label": "Tissue", "start": 62 }, { "end": 30, "label": "CellType", "start": 25 }, { "end": 151, "label": "CellType", "start": 14...

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[ { "tags": [ "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "B-Tissue", "I-Tissue", "O", "B-Tissue", "I-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O",...

The AS pattern in hCNS-SCns may represent a transient, early neuronal molecular change.

[ { "end": 27, "label": "CellType", "start": 18 }, { "end": 69, "label": "Tissue", "start": 61 }, { "end": 25, "label": "CellType", "start": 18 } ]

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[ { "tags": [ "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "B-Tissue", "O", "O", "O" ], "tokens": [ "The", "AS", "pattern", "in", "hCNS-SCns", "may", "repr...

Functional and Expression Characteristics of REAP[+] GenesIn total, 1,500 genes were identified that contained 1,737 REAP[+] exons, 68% of which lacked prior transcript (EST/cDNA) evidence for AS.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

To determine whether genes that contained REAP[+] exons, which we refer to as REAP[+] genes, are biased toward particular biological activities, REAP[+] genes were compared to a set of REAP analyzed genes not found to have REAP[+] exons (REAP[−] genes).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

A Gene Ontology analysis revealed that REAP[+] genes are enriched for GO molecular function categories “ATP binding,” “helicase activity,” “protein serine/theronine kinase activity,” “small GTPase regulatory/interacting protein activity,” and “thyroid hormone receptor binding” (Table 1).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

In terms of GO biological process categories, REAP[+] genes were more frequently involved in “ubiquitin cycle.”

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "terms", "of", "G...

Similar results were obtained when we compared REAP[+] genes to all human genes that did not contain REAP[+] exons (Table 1) [55].Table 1Significantly Enriched Gene Ontology Terms in REAP[+] Genes (Cutoff of Two Significant “Outliers” per Probeset)Next we asked if REAP[+] genes are differentially expressed in hESCs com...

[ { "end": 332, "label": "CellType", "start": 329 }, { "end": 316, "label": "CellType", "start": 311 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

For this analysis, the t-statistics computed above measuring the enrichment of a gene in hESCs relative to NPs was utilized for only REAP-analyzed genes.

[ { "end": 110, "label": "CellType", "start": 107 }, { "end": 94, "label": "CellType", "start": 89 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "...

At a defined absolute-valued cutoff, genes were divided into three categories: “enriched in hESCs,” “enriched in NP,” or “unchanged” (Figure 8A).

[ { "end": 97, "label": "CellType", "start": 92 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Increasing the t-statistic cutoff from one to five, the fraction of REAP[+] genes relative to REAP-analyzed genes remained constant in the “unchanged” categories (Figure 8B).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

However, the fraction of REAP[+] exons decreased significantly in “enriched in hESCs” and “enriched in NPs” categories.

[ { "end": 106, "label": "CellType", "start": 103 }, { "end": 84, "label": "CellType", "start": 79 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O" ], "tokens"...

If we increased the cutoffs on genes that were randomly assigned as REAP[+] and REAP[−], controlling for the same number of genes in each category, we observed that the fraction of REAP[+] exons remained unchanged for all three categories (Figure 8C).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

To illustrate, at a cutoff of five, 10% (29 of 267) of enriched NP genes were REAP[+] genes and 8.8% (102 of 1,162) of enriched hESC genes were REAP[+], significantly different (p < 0.000005) from the random control where ∼14% of enriched NP and enriched hESC genes were REAP[+].

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

At a cutoff of five, 14% (1,368 of 9,636) of genes that were expressed at similar levels between hESCs and NPs were REAP[+].

[ { "end": 110, "label": "CellType", "start": 107 }, { "end": 102, "label": "CellType", "start": 97 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "B-CellType", "...

Our results suggested that a strategy of focusing on differentially expressed genes would miss at least 14% of transcriptionally unchanged genes that may nevertheless have functional AS differences between hESCs and NPs.

[ { "end": 211, "label": "CellType", "start": 206 }, { "end": 219, "label": "CellType", "start": 216 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Figure 8Analysis of REAP[+] Genes Relative to Transcriptional Differences(A) Histogam of t-statistics computed from gene-level signal estimates measuring the enrichment of genes in hESC and in NP.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Genes on the right of the vertical line at 5 were designated enriched in hESC and genes on the left of the vertical line at −5 were designated enriched in NP; genes in between −5 and 5 were designated as “unchanged” or expressed similarly in hESC and NP.(B) Vertical bars representing the percentage of REAP[+] genes out...

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Similar representation as in (B).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Similar", "representation", "as", "in", "(", "B", ")", "." ] } ]

Conserved Intronic Splicing Regulatory Elements Proximal to REAP[+] hESC and NP ExonsMany, if not most, alternative exons undergo cell type–specific regulation by the binding of trans-factors to splicing regulatory cis-elements located proximal to or within the exons.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

As many tissue-specific splicing cis-regulatory elements were localized in intronic regions of AS exons, we focused on the identification of intronic splicing regulatory elements (ISREs) proximal to REAP[+] exons.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

In addition, we wanted to identify both common and cell type–specific ISREs.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "In", "addition", ",", "we", "wanted", "to", "identify", ...

Three sets of exons were generated: (i) REAP[+] exons that were predicted to be included in NPs and skipped in hESCs (REAP[+]NP); (ii) REAP[+] exons that were predicted to be included in hESCs and skipped in NPs (REAP[+]hESC); and (iii) all REAP[−] exons.

[ { "end": 95, "label": "CellType", "start": 92 }, { "end": 116, "label": "CellType", "start": 111 }, { "end": 211, "label": "CellType", "start": 208 }, { "end": 192, "label": "CellType", "start": 187 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "B-CellType", "...

Regions of 400 base pairs flanking the exons were targeted for search.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Regions", "of", "400", "base", "pairs", "flanking", "the", "exons", "were", ...

Initially, 5-mers that were significantly enriched between the upstream and downstream intronic regions of REAP[+]NP and REAP[+]ES relative to REAP[−] exons were enumerated.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...

We were not able to identify 5-mers that were statistically significantly different.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "We", "were", "not", "able", "to", "identify", "5-mers", "that", "were", "s...

Next, we focused on splicing signals that were conserved across mammalian genomes as a way of enhancing the signal of detecting functional splicing regulatory sequences [66].

[ { "end": 73, "label": "Tissue", "start": 64 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "...

Exons that were orthologous across human, dog, rat, and mouse were obtained and the flanking intronic regions were aligned (400 bases upstream and downstream separately; Figure 9A).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

We enumerated k-mers that were perfectly conserved across all four genomes in the upstream (and downstream) intronic regions.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "We", "enumerated", "k-mers",...

Each conserved k-mer was attributed a χ score representing its enrichment in a set of exons relative to another set of exons.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Each", "cons...

The higher the score, the more frequent the conserved k-mer was in the first set relative to the second set.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "higher", "...

As a negative control, the associations between REAP scores and exons were shuffled.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "As", "a", "negative", "control", ",", "the", "associations", "be...

The enrichment scores for all downstream intronic 5-mers for shuffled REAP[+]NP versus set REAP[−] exons (x-axis), and for shuffled REAP[+]ES exons versus REAP[−] exons (y-axis) were displayed (Figure 9B).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

At a χ cutoff of three, which corresponded to a p-value of 0.0015, the majority of 5-mers were not significantly enriched in either shuffled set.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Confident that no association of k-mers with shuffled REAP exons were found; we repeated the analyses for upstream and downstream intronic 5-mers for the original unshuffled sets.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

We identified 68 conserved 5-mers enriched upstream of REAP[+]NP exons; and 34 5-mers enriched upstream of REAP[+]ES exons (Figure 9C; Table S4).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ...

Of the 5-mers that were significantly enriched upstream of REAP[+]NP exons, we identified a U-rich motif (UUUUU), a GU-rich motif (GUGUG), and a CU-rich motif (CCUCU, CUCUC, UCUCU, GCUCU).

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

It is known that the heterogeneous ribonucleoprotein C (hnRNP C) binding site obtained by SELEX is five “U”s [67].

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ ...

GU-rich sequences in flanking intronic regions were shown to bind to splicing factor ETR-3 to regulate AS [68].

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "GU-rich", "sequences", "in",...

CU-rich sequences were shown to bind the splicing factor PTB [69].

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "CU-rich", "sequences", "were", "shown", "to", "bind", "the", "splicing", ...

Of the 5-mers enriched upstream of REAP[+]ES exons, we observed CUAAC, which resembled the splicing branch-signal.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Of", "the", "5-mers", "enriched", "ups...

Of the six 5-mers that were enriched upstream of both REAP[+]NP and REAP[+]ES exons, we identified GCAUG, which was previously shown to be an intronic splicing cis-element for the mammalian fibronectin and calcitonin/CGRP genes [70–72].

[ { "end": 189, "label": "Tissue", "start": 180 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

More recently, both mammalian Fox1 and 2 have been demonstrated to regulate alternatively spliced exons via UGCAUG binding sites in neighboring introns in neuronal cell cultures [73].Figure 9Conserved Intronic cis-Elements Enriched Proximal to REAP[+] Alternative Exons(A) Schematic describing the enumeration of introni...

[ { "end": 369, "label": "Tissue", "start": 360 }, { "end": 163, "label": "Tissue", "start": 155 }, { "end": 29, "label": "Tissue", "start": 20 } ]

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[ { "tags": [ "O", "O", "O", "O", "B-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-Tissue", "O", ...

Red and green horizontal bars represent conserved intronic elements and nonconserved elements, respectively.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Red", "and", "green", "horizontal", "bars", "represent", "conserved", ...

Internal exons were divided into REAP[+]NP, REAP[+]ES, and REAP[−] exons.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Internal", "exons", "were", "divided", "into", "REAP[+]NP", ",", "REAP[+]ES...

The χ statistic was computed to represent the enrichment of conserved elements in intronic regions flanking REAP[+]NP versus REAP[−] exons (x-axis), and REAP[+]ES versus REAP[−] exons (y-axis).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

The sign represented the direction of change, i.e., positive if enriched in introns flanking REAP[+] versus REAP[−] exon.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "The", "sign"...

Each conserved 5-mer was associated with two numbers: the enrichment in introns proximal to REAP[+]NP versus REAP[−] exons (x-axis), and REAP[+]ES versus REAP[−] exons (y-axis).(B) Downstream intronic regions, where the association between REAP[+] designation and the exons was shuffled.(C) Upstream intronic regions.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Circled 5-mers in the upper right quadrant represent conserved 5-mers enriched in the upstream intronic regions of REAP[+]NP and REAP[+]ES exons.(D) Downstream intronic regions.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...

Circled 5-mers in the upper right quadrant represent conserved 5-mers enriched in the downstream intronic regions of REAP[+]NP and REAP[+]ES exons.

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "Circled", "5-mers", ...

Eighteen conserved 5-mers were significantly enriched in the downstream introns of REAP[+]ES exons; and 76 5-mers were enriched downstream of REAP[+]NP exons (Table S4, Figure 9D).

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

We identified a motif CUCAU resembling the Nova binding site YCAY [74], and a G-rich motif (AGGGG, GGGGA, GGGGC, GGGGG, GGGGU) enriched in the introns downstream of REAP[+]ES exons.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

G-rich motifs had previously been shown to be part of a bipartite signal that silences AS exons [75].

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tokens": [ "G-rich", "motifs", "had", ...

Of the five 5-mers that were enriched downstream of both REAP[+]NP and REAP[+]ES exons, GCAUG and a U-rich motif (UUUUU) were identified.

[]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ], "tok...

We concluded that potential ISREs were enriched proximal to a subset of REAP[+] exons; in particular, the Fox1/2 binding site GCUAG may play a regulatory role in controlling AS events in hESCs and NPs.

[ { "end": 200, "label": "CellType", "start": 197 }, { "end": 192, "label": "CellType", "start": 187 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

The ability of ESCs to generate all three embryonic germ layers has raised the exciting possibility that hESCs may become an unlimited source of cells for transplantation therapies involving organs or tissues such as the liver, pancreas, blood, and nervous system, and become tools to explore the molecular mechanisms of...

[ { "end": 244, "label": "Tissue", "start": 239 }, { "end": 237, "label": "Tissue", "start": 229 }, { "end": 111, "label": "CellType", "start": 106 }, { "end": 264, "label": "Tissue", "start": 250 }, { "end": 20, "label": "CellType", "start":...

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "I-Tissue", "I-Tissue", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", ...

Despite such interests, relatively little is understood about the molecular mechanisms defining their pluripotency and the molecular changes important for hESCs to differentiate into specific cell types.

[ { "end": 160, "label": "CellType", "start": 155 } ]

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[ { "tags": [ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-CellType", "O", "O", "O", "O", ...