genbio-ai/IsoformExpression-Enformer-AIDO.RNA-1.6B-CDS-ESM2-150M-ConcatFusion-rna-isoform-expression-ckpt
Updated • 10
transcript_id string | gene_id string | labels_0 float64 | labels_1 float64 | labels_2 float64 | labels_3 float64 | labels_4 float64 | labels_5 float64 | labels_6 float64 | labels_7 float64 | labels_8 float64 | labels_9 float64 | labels_10 float64 | labels_11 float64 | labels_12 float64 | labels_13 float64 | labels_14 float64 | labels_15 float64 | labels_16 float64 | labels_17 float64 | labels_18 float64 | labels_19 float64 | labels_20 float64 | labels_21 float64 | labels_22 float64 | labels_23 float64 | labels_24 float64 | labels_25 float64 | labels_26 float64 | labels_27 float64 | labels_28 float64 | labels_29 float64 | chromosome int64 | tss int64 | tes int64 | strand string | coding_start float64 | coding_end float64 | splice_sites string | rna_seq string | protein_seq string | dna_seq string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000367770 | ENSG00000000457 | 0.45651 | -0.296923 | 0.002882 | -0.409102 | 0.647377 | 0.929601 | 0.913451 | 0.58141 | 0.604809 | -0.051248 | 0.045928 | 0.908046 | 0.462883 | 0.979782 | 0.024463 | 0.283895 | 0.0556 | 0.496298 | 0.455828 | 1.065435 | 1.298247 | 0.945113 | -0.248402 | 0.676774 | 0.797877 | 0.566702 | 0.289469 | 1.100223 | 0.786481 | 0.768831 | 1 | 169,888,888 | 169,853,074 | - | 48 | 2,277 | [213, 399, 513, 570, 673, 785, 863, 1003, 1188, 1360, 1522, 2217] | "CTGCTTGGCTTTGAGGAAGAGTGGCAGTACTGCCTCACTGCATAAGGGATGGGATCAGAGAACAGTGCTTTAAAGAGCTATACACTGAGAGAACCACCA(...TRUNCATED) | "MGSENSALKSYTLREPPFTLPSGLAVYPAVLQDGKFASVFVYKRENEDKVNKAAKHLKTLRHPCLLRFLSCTVEADGIHLVTERVQPLEVALETLSSAE(...TRUNCATED) | "TGTCAGCAATTACACTTACTTTTGAAGTGCCATCATAGCAATCAAATTAAAGACATACTCTTTCATGTGGAGTTTGAACTAAACATTGCTTTTTTAAAT(...TRUNCATED) |
ENST00000367771 | ENSG00000000457 | 0.4863 | -0.371569 | 0.432217 | -0.603393 | 0.832064 | 0.708716 | 0.882358 | 0.709133 | 0.871284 | 0.081044 | 0.523066 | 0.904649 | 0.488111 | 0.670622 | 0.07125 | 0.450368 | 0.431594 | 0.623593 | 0.681499 | 0.829148 | 0.472573 | 0.816795 | 0.089257 | 0.461394 | 0.706908 | 0.155045 | 0.095707 | 0.929091 | 0.743043 | 0.874319 | 1 | 169,893,896 | 169,849,631 | - | 159 | 2,226 | [109, 324, 510, 624, 681, 784, 896, 974, 1114, 1299, 1471, 2166] | "GTAGTGGCCACAGCCTTACAGGCAGGCAGGGGTGGTTGGTGTCAACAGGGGGGCCAACAGGGTACCAGAGCCAAGACCCTCGGCCTCCTCCCCCGCCGC(...TRUNCATED) | "MGSENSALKSYTLREPPFTLPSGLAVYPAVLQDGKFASVFVYKRENEDKVNKAAKHLKTLRHPCLLRFLSCTVEADGIHLVTERVQPLEVALETLSSAE(...TRUNCATED) | "TGACCGCTTTAAATCAATGTTTGCATACACTGACTGTATACCACAGGTAAGTGGTTTAAGTGTTTTATGAAAAACATTTAACAAATATATATATTTTTT(...TRUNCATED) |
ENST00000367772 | ENSG00000000457 | 0.404075 | 0.6098 | 0.576863 | -0.718278 | 0.826225 | 0.51273 | 0.459004 | 0.503409 | 0.788363 | -1.264949 | 0.264794 | 0.669293 | 0.448955 | -0.100558 | -1.357413 | 0.506482 | 0.148026 | 0.457748 | 0.549816 | 0.146111 | -0.387391 | 0.634559 | -0.037103 | -0.318016 | 0.445391 | -0.556988 | -0.334469 | 0.529138 | 0.559673 | 1.003117 | 1 | 169,893,959 | 169,853,074 | - | 222 | 2,451 | [172, 387, 573, 687, 744, 847, 959, 1037, 1177, 1362, 1534, 1696, 2391] | "TGTCCCGTTTCCGGACCCGTCTCTATGGTGTAGGAGAAACCCGGCCCCCAGAAGATTGTGGGTGTAGTGGCCACAGCCTTACAGGCAGGCAGGGGTGGT(...TRUNCATED) | "MGSENSALKSYTLREPPFTLPSGLAVYPAVLQDGKFASVFVYKRENEDKVNKAAKHLKTLRHPCLLRFLSCTVEADGIHLVTERVQPLEVALETLSSAE(...TRUNCATED) | "ATTCCTAGGCAATGACAACTACAAACAAATAGCAATGTGTGTTCTTTACCACATAAGCATGGATGACCGCTTTAAATCAATGTTTGCATACACTGACTG(...TRUNCATED) |
ENST00000423670 | ENSG00000000457 | -1.149057 | -0.853836 | -0.928967 | -2.632476 | -1.033969 | -0.530292 | -1.333707 | -0.997558 | -1.003534 | -2.316749 | -1.138638 | -0.708999 | -0.936221 | -1.227284 | -2.865946 | -0.533179 | -1.581071 | -0.80097 | -1.197954 | -0.78809 | -0.558112 | -0.959953 | -1.559711 | -1.105047 | -1.704726 | -1.129082 | -1.729963 | -0.960421 | -1.188938 | -0.560274 | 1 | 169,894,267 | 169,854,511 | - | null | null | [261, 476, 662, 776, 833, 936, 1048, 1126, 1266, 1451, 1623] | "GCACCTCTACTGTTTGCTACAAGTGGCCAGCAGCCATTTTGGATTTGGGCGGAAATGAAATTAAAACTGTGCTGTTAAAAGCCTAAAAATTCAAGTCAA(...TRUNCATED) | "MGSENSALKSYTLREPPFTLPSGLAVYPAVLQDGKFASVFVYKRENEDKVNKAAKHLKTLRHPCLLRFLSCTVEADGIHLVTERVQPLEVALETLSSAE(...TRUNCATED) | "TAAAGATGGGGAGGCTAATGACCCAATTGTTTTTATATTGGACTCATGAAAATAATTAATTCCTATGGTTAATTTTCTTTTTCAAAACTATACCTTGGG(...TRUNCATED) |
ENST00000470238 | ENSG00000000457 | -0.427529 | -1.40307 | -0.30008 | -1.808157 | -0.084728 | -0.018728 | -0.116568 | -0.174682 | -0.21986 | -1.484992 | -1.198487 | -0.131066 | -0.469871 | -1.235957 | -1.501557 | -0.679341 | -1.008614 | -0.562845 | -0.906861 | -0.361617 | -0.164162 | 0.070526 | -1.02734 | -0.863066 | -0.110075 | -1.415156 | -1.214178 | -0.105249 | -0.306993 | -0.062783 | 1 | 169,893,952 | 169,859,119 | - | null | null | [165, 380, 566, 680, 737, 840, 1041, 1119, 1259, 1444] | "TTTCCGGACCCGTCTCTATGGTGTAGGAGAAACCCGGCCCCCAGAAGATTGTGGGTGTAGTGGCCACAGCCTTACAGGCAGGCAGGGGTGGTTGGTGTC(...TRUNCATED) | null | "GGCAATGACAACTACAAACAAATAGCAATGTGTGTTCTTTACCACATAAGCATGGATGACCGCTTTAAATCAATGTTTGCATACACTGACTGTATACCA(...TRUNCATED) |
ENST00000286031 | ENSG00000000460 | -3.057565 | -4.417229 | -3.726165 | -4.135885 | -2.889699 | -3.336851 | -2.872651 | -2.876136 | -3.016162 | -3.054229 | -2.828 | -2.615068 | -2.993044 | -2.421682 | -3.374176 | -2.961923 | -2.836142 | -2.828329 | -2.426616 | -3.131529 | -1.549027 | -2.591627 | -2.665849 | -2.604823 | -3.221936 | -3.240954 | -3.441703 | -3.419415 | -2.757766 | -3.816496 | 1 | 169,795,409 | 169,854,080 | + | 700 | 3,262 | "[574, 676, 765, 870, 1011, 1177, 1262, 1401, 1482, 1547, 1696, 1826, 2013, 2096, 2148, 2238, 2424, (...TRUNCATED) | "GGCTTTGGCCCTGGAAAGCCTCGCGGACGTGTTCTGACCCAAGGTTTTAGCAGTGGATGTGGCGTTTTCTTCCATTCCTTCTTTCAGTTTTTCTGTACT(...TRUNCATED) | "MFLPHMNHLTLEQTFFSQVLPKTVKLFDDMMYELTSQARGLSSQNLEIQTTLRNILQTMVQLLGALTGCVQHICATQESIILENIQSLPSSVLHIIKST(...TRUNCATED) | "TCAGAGCTAGATCTGAGACCCTCTCCTACCAAGTATATAAAACTTTGTGACATACATTTTTGTGCCATAACTTCAACCTTGGTTCCAAATGATTTTTGT(...TRUNCATED) |
ENST00000359326 | ENSG00000000460 | -1.073327 | -2.912832 | -1.251283 | -2.301702 | -0.681745 | -0.565774 | -0.867418 | -0.75205 | -0.807378 | -2.136115 | -1.110475 | -0.4801 | -1.061168 | -0.842195 | -1.906867 | -0.993141 | -1.178797 | -1.092886 | -0.89462 | -0.633151 | 0.42678 | -0.722951 | -0.873044 | -1.145323 | -0.774381 | -1.027042 | -1.517253 | -0.660843 | -1.838921 | -0.452849 | 1 | 169,795,040 | 169,854,080 | + | 356 | 2,918 | "[75, 230, 332, 421, 526, 667, 833, 918, 1057, 1138, 1203, 1352, 1482, 1669, 1752, 1804, 1894, 2080,(...TRUNCATED) | "ACTGCGAGTTTCCGGTCTGGGCTTTGGCGGGTCTGGTTTGAAGCTCTCCTGTTTGACGAAAGTATGTCTCAGGAAGGCTGGAGTCTTTCTGAAAGAGTT(...TRUNCATED) | "MFLPHMNHLTLEQTFFSQVLPKTVKLFDDMMYELTSQARGLSSQNLEIQTTLRNILQTMVQLLGALTGCVQHICATQESIILENIQSLPSSVLHIIKST(...TRUNCATED) | "ACTAATACAGAACAGACATGTTGATGCAGATGCCTCCTGAGGTTCCATTCCATTCTCCGTGCTACTCAAGAAGACAGAATTGCTAAATTGCCTGGTGGC(...TRUNCATED) |
ENST00000413811 | ENSG00000000460 | -0.556756 | -1.492788 | -0.587656 | -1.869355 | -0.418784 | -0.807155 | -0.534726 | -0.105593 | -1.28525 | -0.580187 | -1.557776 | -1.272773 | -0.896514 | -0.42395 | -3.301231 | -0.878827 | -1.672441 | -0.788833 | -0.787649 | -1.269698 | 1.611174 | 0.358772 | -0.755864 | -1.130877 | -0.864357 | -1.905634 | -2.708798 | -0.438758 | -0.910502 | -0.64462 | 1 | 169,795,921 | 169,853,037 | + | 1,018 | 2,611 | "[62, 164, 253, 358, 499, 665, 750, 831, 896, 1045, 1175, 1362, 1445, 1497, 1587, 1773, 1896, 1992, (...TRUNCATED) | "ACATTCTTGATTGGTCTCATGCCTTTGTGGTTGTAAATGTGCCTGGAATCCTAGCCTTTCATGGTTTGTTCTGAGTAATGAATACCCTATTACTATGAT(...TRUNCATED) | "MQVVLDSKLDLPCELQFPQCLLLVVVMDKLPSQPKEVQTLWCTDSQVSETTTRISLLKAVFYSFEQCSGELSLPVHLQGLKSKGKAEVAVTLYQHVCVH(...TRUNCATED) | "GTTAAAGAGGCATAATAATTGTATCATCCTCATTGGGTTGATAAAATAAAATATTTCCAAGTATTTAGTTCAGGTCCTAGCACGTAGACAGTGTTGCAT(...TRUNCATED) |
ENST00000459772 | ENSG00000000460 | 0.155889 | -1.287344 | 0.008209 | -0.917144 | 0.743325 | 0.519959 | 0.33715 | 0.141035 | 0.063648 | -0.373121 | -0.394043 | 0.35722 | 0.048111 | 0.39678 | -0.984798 | 0.098378 | -0.277425 | 0.120214 | 0.143145 | 0.477208 | 1.484425 | 0.798112 | -0.088269 | 0.159924 | 0.660073 | -0.423913 | -0.480596 | 0.766738 | 0.67752 | 0.224746 | 1 | 169,795,079 | 169,854,080 | + | 24 | 195 | "[134, 174, 279, 420, 549, 634, 773, 854, 919, 1068, 1198, 1385, 1468, 1520, 1610, 1796, 1919, 2015,(...TRUNCATED) | "GAAGCTCTCCTGTTTGACGAAAGTATGTCTCAGGAAGGTGCGGTCCCAGCTAGCGCGGTTCCCCTGGAAGAATTAAGTAGCTGGCCAGAGGAGCTATGC(...TRUNCATED) | MSQEGAVPASAVPLEELSSWPEELCRRELPSVLPRLLSLSQHSDSWIEHIHCEIIR | "AGGTTCCATTCCATTCTCCGTGCTACTCAAGAAGACAGAATTGCTAAATTGCCTGGTGGCAAGACCCAATATGTCCATTCAAGTGTTTATCCCTTCCCA(...TRUNCATED) |
ENST00000466580 | ENSG00000000460 | -6.527864 | -6.100401 | -4.811278 | -7.790638 | -7.556818 | -6.453907 | -6.449393 | -6.432067 | -9.21034 | -6.597192 | -8.008696 | -7.635808 | -5.341521 | -9.21034 | -7.739324 | -6.230477 | -7.286153 | -6.012008 | -6.343718 | -9.21034 | -9.21034 | -5.47958 | -7.131303 | -5.392123 | -9.21034 | -9.21034 | -9.21034 | -9.21034 | -9.21034 | -5.999113 | 1 | 169,795,079 | 169,821,719 | + | 24 | 195 | [134, 174, 279, 420, 549, 634, 773] | "GAAGCTCTCCTGTTTGACGAAAGTATGTCTCAGGAAGGTGCGGTCCCAGCTAGCGCGGTTCCCCTGGAAGAATTAAGTAGCTGGCCAGAGGAGCTATGC(...TRUNCATED) | MSQEGAVPASAVPLEELSSWPEELCRRELPSVLPRLLSLSQHSDSWIEHIHCEIIR | "AGGTTCCATTCCATTCTCCGTGCTACTCAAGAAGACAGAATTGCTAAATTGCCTGGTGGCAAGACCCAATATGTCCATTCAAGTGTTTATCCCTTCCCA(...TRUNCATED) |
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Multi-modal transcript isoform expression dataset
We curated the human transcript isoform expression dataset from the GTEx portal following the preprocessing pipeline in Garau-Luis et al. (2024). We downloaded the RNA-seq Transcript TPMs file from the bulk tissue expression in GTEx Analysis V8. The table contains transcript expression collected from 30 non-diseased tissues in nearly 1000 human individuals. We averaged the transcript expression measurements across individuals to obtain population-level tissue-specific transcript expression data. For each transcript, we used the associated Ensembl transcript id to retrieve a DNA sequence of length 197k centering on the transcript start site using the human reference genome GRCh38. We also retrieved the protein sequence for each transcript if it encodes a protein. For each sample in the dataset, we have a DNA sequence, an RNA sequence, a protein sequence (potentially), and expression levels of the transcript across 30 tissues. Furthermore, we split the dataset into training, validation and test sets based on the chromosomes. In specific, we used chromosomes 1-19 for training, 20 for validation and 21-22 for test. The training, validation, and test sets contain 175k, 4k and 6.5k samples respectively. We performed $log_2(0.0001+x)$ transform for the labels.
Details about dataset
- training set:
train_i.tsv, where i=1,...,19 denotes chromosome i. - validation set:
validation.tsv, corresponds to chromosome 20. - test set:
test.tsv, corresponds to chromosomes 21 and 22.
Columns in each file:
transcript_idgene_idlabels_i(i=0,...,29): transcript isoform expression level in 30 tissues.chromosometss: transcription start sitetes: transcription end sitestrandrna_seqprotein_seqdna_seq: of length 197k, centered at the TSS of the transcript
Update Note — 2026-07-10
- Fixed a bug in transcript coordinate annotation for genes on the negative (
-) strand: the TSS should correspond to the transcript end, and the TES should correspond to the transcript start. In the previous version, these coordinates were reversed, which affecteddna_seqfor transcripts on the negative strand. - Added three new columns:
coding_start,coding_end, andsplice_sites.
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