Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
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is_cap
bool
is_alpha
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ends_wp
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cit_qc
bool
lgtm
bool
__index_level_0__
int64
2
INTRODUCTION
1
2
[ "B2", "B2", "B17", "B2" ]
17,317,683
pmid-15860776|pmid-15860776|pmid-12458088|pmid-15860776
Putative RNA patterns inferred from sequence must be validated in terms of their tertiary structure.
[ "2", "2", "17", "2" ]
100
2,400
0
false
Putative RNA patterns inferred from sequence must be validated in terms of their tertiary structure.
[]
Putative RNA patterns inferred from sequence must be validated in terms of their tertiary structure.
true
true
true
true
true
413
2
INTRODUCTION
1
2
[ "B2", "B2", "B17", "B2" ]
17,317,683
pmid-15860776|pmid-15860776|pmid-12458088|pmid-15860776
For instance, one needs to establish the base-pairing substitution rules that are constrained by the structural context, which may include subtle factors such as base stacking outside the canonical stems (2,17).
[ "2", "2", "17", "2" ]
211
2,401
0
false
For instance, one needs to establish the base-pairing substitution rules that are constrained by the structural context, which may include subtle factors such as base stacking outside the canonical stems.
[ "2,17" ]
For instance, one needs to establish the base-pairing substitution rules that are constrained by the structural context, which may include subtle factors such as base stacking outside the canonical stems.
true
true
true
true
true
413
2
INTRODUCTION
1
2
[ "B2", "B2", "B17", "B2" ]
17,317,683
pmid-15860776|pmid-15860776|pmid-12458088|pmid-15860776
Isostericity matrices are useful in such situations (2).
[ "2", "2", "17", "2" ]
56
2,402
1
false
Isostericity matrices are useful in such situations.
[ "2" ]
Isostericity matrices are useful in such situations.
true
true
true
true
true
413
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21" ]
17,317,683
pmid-10592235|NA|NA|pmid-16679452
However, now that RNA crystallographic data accumulate rapidly (18), we can now conceive a direct inference of RNA tertiary structure information.
[ "18", "19", "20", "21" ]
146
2,403
1
false
However, now that RNA crystallographic data accumulate rapidly, we can now conceive a direct inference of RNA tertiary structure information.
[ "18" ]
However, now that RNA crystallographic data accumulate rapidly, we can now conceive a direct inference of RNA tertiary structure information.
true
true
true
true
true
414
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21" ]
17,317,683
pmid-10592235|NA|NA|pmid-16679452
Here, we show that a graph-grammar (19,20) has the required complexity to encode RNA motifs in the context of their tertiary structures.
[ "18", "19", "20", "21" ]
136
2,404
0
false
Here, we show that a graph-grammar has the required complexity to encode RNA motifs in the context of their tertiary structures.
[ "19,20" ]
Here, we show that a graph-grammar has the required complexity to encode RNA motifs in the context of their tertiary structures.
true
true
true
true
true
414
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21" ]
17,317,683
pmid-10592235|NA|NA|pmid-16679452
The graph-grammar of an RNA motif can parse and derive RNA sequences that are compatible to it (i.e.
[ "18", "19", "20", "21" ]
100
2,405
0
false
The graph-grammar of an RNA motif can parse and derive RNA sequences that are compatible to it (i.e.
[]
The graph-grammar of an RNA motif can parse and derive RNA sequences that are compatible to it (i.e.
true
true
true
true
true
414
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21" ]
17,317,683
pmid-10592235|NA|NA|pmid-16679452
sequences that are predicted to fold in it).
[ "18", "19", "20", "21" ]
44
2,406
0
false
sequences that are predicted to fold in it).
[]
sequences that are predicted to fold in it).
false
true
true
true
false
414
3
INTRODUCTION
1
21
[ "B18", "B19", "B20", "B21" ]
17,317,683
pmid-10592235|NA|NA|pmid-16679452
The graph-grammar of an RNA motif is built of the fundamental structural elements (21) of an instance of its 3D structure (The 3D structure of an RNA is defined by its atomic coordinates in 3D space.)
[ "18", "19", "20", "21" ]
200
2,407
1
false
The graph-grammar of an RNA motif is built of the fundamental structural elements of an instance of its 3D structure (The 3D structure of an RNA is defined by its atomic coordinates in 3D space.)
[ "21" ]
The graph-grammar of an RNA motif is built of the fundamental structural elements of an instance of its 3D structure (The 3D structure of an RNA is defined by its atomic coordinates in 3D space.)
true
true
false
true
false
414
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21" ]
17,317,683
pmid-10592235|NA|NA|pmid-16679452
or alternatively tertiary structure.
[ "18", "19", "20", "21" ]
36
2,408
0
false
or alternatively tertiary structure.
[]
or alternatively tertiary structure.
false
true
true
true
false
414
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
In this work, the building and use of a graph-grammar are exemplified with the classical sarcin–ricin motif.
[ "22", "23" ]
108
2,409
0
false
In this work, the building and use of a graph-grammar are exemplified with the classical sarcin–ricin motif.
[]
In this work, the building and use of a graph-grammar are exemplified with the classical sarcin–ricin motif.
true
true
true
true
true
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
This motif is found in the sarcin–ricin loop (22,23) (ribosomal loop E), conserved among 23–28S ribosomal RNAs (rRNAs).
[ "22", "23" ]
119
2,410
0
false
This motif is found in the sarcin–ricin loop (ribosomal loop E), conserved among 23–28S ribosomal RNAs (rRNAs).
[ "22,23" ]
This motif is found in the sarcin–ricin loop (ribosomal loop E), conserved among 23–28S ribosomal RNAs (rRNAs).
true
true
true
true
true
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
We chose the sarcin–ricin motif for the diversity of its nucleotide interactions.
[ "22", "23" ]
81
2,411
0
false
We chose the sarcin–ricin motif for the diversity of its nucleotide interactions.
[]
We chose the sarcin–ricin motif for the diversity of its nucleotide interactions.
true
true
true
true
true
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
It includes all base-stacking types and many non-canonical base pairs.
[ "22", "23" ]
70
2,412
0
false
It includes all base-stacking types and many non-canonical base pairs.
[]
It includes all base-stacking types and many non-canonical base pairs.
true
true
true
true
true
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
Using the sarcin–ricin graph-grammar, we derived four putative sarcin–ricin sequences, of which three are found in published X-ray crystallographic structures.
[ "22", "23" ]
159
2,413
0
false
Using the sarcin–ricin graph-grammar, we derived four putative sarcin–ricin sequences, of which three are found in published X-ray crystallographic structures.
[]
Using the sarcin–ricin graph-grammar, we derived four putative sarcin–ricin sequences, of which three are found in published X-ray crystallographic structures.
true
true
true
true
true
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
We then compared the derived sequences against an alignment of over 800 bacterial 23S
[ "22", "23" ]
85
2,414
0
false
We then compared the derived sequences against an alignment of over 800 bacterial 23S
[]
We then compared the derived sequences against an alignment of over 800 bacterial 23S
true
true
false
true
false
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
The comparison highlighted few possible alternative alignments that we could not refute by tertiary structure predictions or 3D modeling.
[ "22", "23" ]
137
2,415
0
false
The comparison highlighted few possible alternative alignments that we could not refute by tertiary structure predictions or 3D modeling.
[]
The comparison highlighted few possible alternative alignments that we could not refute by tertiary structure predictions or 3D modeling.
true
true
true
true
true
415
4
INTRODUCTION
1
22
[ "B22", "B23" ]
17,317,683
pmid-7897662|pmid-8415744
Further analyses and laboratory experiments will be needed to confirm the right alignment and to bring light about the structural events that occurred during the evolution.
[ "22", "23" ]
172
2,416
0
false
Further analyses and laboratory experiments will be needed to confirm the right alignment and to bring light about the structural events that occurred during the evolution.
[]
Further analyses and laboratory experiments will be needed to confirm the right alignment and to bring light about the structural events that occurred during the evolution.
true
true
true
true
true
415
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
InterPro (1) incorporates the major protein signature databases into a single resource.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
87
2,417
1
false
InterPro incorporates the major protein signature databases into a single resource.
[ "1" ]
InterPro incorporates the major protein signature databases into a single resource.
true
true
true
true
true
416
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
These include: PROSITE (2), which uses regular expressions and profiles, PRINTS (3), which uses Position Specific Scoring Matrix-based (PSSM-based) fingerprints, ProDom (4), which uses automatic sequence clustering, and Pfam (5), SMART (6), TIGRFAMs (7), PIRSF (8), SUPERFAMILY (9), Gene3D (10) and PANTHER (11), all of ...
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
358
2,418
1
false
These include: PROSITE, which uses regular expressions and profiles, PRINTS, which uses Position Specific Scoring Matrix-based (PSSM-based) fingerprints, ProDom, which uses automatic sequence clustering, and Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER, all of which use hidden Markov models (HMMs).
[ "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
These include: PROSITE, which uses regular expressions and profiles, PRINTS, which uses Position Specific Scoring Matrix-based (PSSM-based) fingerprints, ProDom, which uses automatic sequence clustering, and Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER, all of which use hidden Markov models (HMMs).
true
true
true
true
true
416
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
Table 1 shows the coverage of each of these member databases.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
61
2,419
0
false
Table 1 shows the coverage of each of these member databases.
[]
Table 1 shows the coverage of each of these member databases.
true
true
true
true
true
416
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
Protein signatures from these databases that describe the same family or domain, in terms of sequence positions and protein coverage are integrated into single InterPro entries, to which are added annotation and cross-references.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
229
2,420
0
false
Protein signatures from these databases that describe the same family or domain, in terms of sequence positions and protein coverage are integrated into single InterPro entries, to which are added annotation and cross-references.
[]
Protein signatures from these databases that describe the same family or domain, in terms of sequence positions and protein coverage are integrated into single InterPro entries, to which are added annotation and cross-references.
true
true
true
true
true
416
0
INTRODUCTION
1
12
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
Annotation includes an abstract, name, short name and GO terms (12) (where applicable).
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
87
2,421
1
false
Annotation includes an abstract, name, short name and GO terms (where applicable).
[ "12" ]
Annotation includes an abstract, name, short name and GO terms (where applicable).
true
true
true
true
true
416
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
Cross-references are provided to specialized databases and protein structural information.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
90
2,422
0
false
Cross-references are provided to specialized databases and protein structural information.
[]
Cross-references are provided to specialized databases and protein structural information.
true
true
true
true
true
416
0
INTRODUCTION
1
13
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
All matches of the protein signatures contributed by member databases against the UniProt Knowledgbase (UniProtKB) (13) are calculated using the InterProScan software (14), which integrates the search algorithms from the member databases into a single package.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
260
2,423
1
false
All matches of the protein signatures contributed by member databases against the UniProt Knowledgbase (UniProtKB) are calculated using the InterProScan software, which integrates the search algorithms from the member databases into a single package.
[ "13", "14" ]
All matches of the protein signatures contributed by member databases against the UniProt Knowledgbase (UniProtKB) are calculated using the InterProScan software, which integrates the search algorithms from the member databases into a single package.
true
true
true
true
true
416
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
The matches are available for viewing in various formats for each InterPro entry.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
81
2,424
0
false
The matches are available for viewing in various formats for each InterPro entry.
[]
The matches are available for viewing in various formats for each InterPro entry.
true
true
true
true
true
416
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
The InterPro data are available for searching and retrieval via a web interface at , and for download by anonymous FTP .
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14" ]
120
2,425
0
false
The InterPro data are available for searching and retrieval via a web interface at, and for download by anonymous FTP.
[]
The InterPro data are available for searching and retrieval via a web interface at, and for download by anonymous FTP.
true
true
true
true
true
416
1
INTRODUCTION
0
null
null
17,202,162
null
Coverage of protein sequences and amino acid residues for each member database
null
78
2,426
0
false
null
null
Coverage of protein sequences and amino acid residues for each member database
true
true
false
true
false
417
2
INTRODUCTION
0
null
null
17,202,162
null
aNot all the methods are integrated into InterPro entries, e.g.
null
63
2,427
0
false
null
null
aNot all the methods are integrated into InterPro entries, e.g.
false
true
true
true
false
418
2
INTRODUCTION
0
null
null
17,202,162
null
for PANTHER, but InterPro provides matches to them in the match XML file.
null
73
2,428
0
false
null
null
for PANTHER, but InterPro provides matches to them in the match XML file.
false
true
true
true
false
418
3
INTRODUCTION
0
null
null
17,202,162
null
bThis is the number of proteins hit by one database only.
null
57
2,429
0
false
null
null
bThis is the number of proteins hit by one database only.
false
true
true
true
false
419
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
InterPro is constantly being updated to keep up with the changing face of Bioinformatics.
[ "15", "5", "16", "17", "18" ]
89
2,430
0
false
InterPro is constantly being updated to keep up with the changing face of Bioinformatics.
[]
InterPro is constantly being updated to keep up with the changing face of Bioinformatics.
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
Two new member databases, PANTHER and Gene3D, have joined the InterPro consortium and their HMMs are being integrated.
[ "15", "5", "16", "17", "18" ]
118
2,431
0
false
Two new member databases, PANTHER and Gene3D, have joined the InterPro consortium and their HMMs are being integrated.
[]
Two new member databases, PANTHER and Gene3D, have joined the InterPro consortium and their HMMs are being integrated.
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
In addition, new database cross-references to CluSTr (15) and Pfam clans (5) have been included, and entries link to the IntAct molecular interaction database (16) where manually curated examples of domain–domain interactions are available.
[ "15", "5", "16", "17", "18" ]
240
2,432
1
false
In addition, new database cross-references to CluSTr and Pfam clans have been included, and entries link to the IntAct molecular interaction database where manually curated examples of domain–domain interactions are available.
[ "15", "5", "16" ]
In addition, new database cross-references to CluSTr and Pfam clans have been included, and entries link to the IntAct molecular interaction database where manually curated examples of domain–domain interactions are available.
true
true
true
true
true
420
4
INTRODUCTION
1
17
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
Proteins with 3D structures modelled by MODBASE (17) and SWISS-MODEL (18) have links to the structure predictions from the match graphical views.
[ "15", "5", "16", "17", "18" ]
145
2,433
1
false
Proteins with 3D structures modelled by MODBASE and SWISS-MODEL have links to the structure predictions from the match graphical views.
[ "17", "18" ]
Proteins with 3D structures modelled by MODBASE and SWISS-MODEL have links to the structure predictions from the match graphical views.
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
These links complement the experimentally determined structures in the protein data bank (PDB).
[ "15", "5", "16", "17", "18" ]
95
2,434
0
false
These links complement the experimentally determined structures in the protein data bank (PDB).
[]
These links complement the experimentally determined structures in the protein data bank (PDB).
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
The web interface has been extended for more advanced searching capabilities, and a web service is now available, providing programmatic access to InterProScan.
[ "15", "5", "16", "17", "18" ]
160
2,435
0
false
The web interface has been extended for more advanced searching capabilities, and a web service is now available, providing programmatic access to InterProScan.
[]
The web interface has been extended for more advanced searching capabilities, and a web service is now available, providing programmatic access to InterProScan.
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
In addition to UniProtKB, InterPro now provides matches to all proteins in the UniProt archive, UniParc, and these are currently available in XML format on the FTP site.
[ "15", "5", "16", "17", "18" ]
169
2,436
0
false
In addition to UniProtKB, InterPro now provides matches to all proteins in the UniProt archive, UniParc, and these are currently available in XML format on the FTP site.
[]
In addition to UniProtKB, InterPro now provides matches to all proteins in the UniProt archive, UniParc, and these are currently available in XML format on the FTP site.
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
The match XML files are also indexed in SRS to allow users to query the data within the SRS interface.
[ "15", "5", "16", "17", "18" ]
102
2,437
0
false
The match XML files are also indexed in SRS to allow users to query the data within the SRS interface.
[]
The match XML files are also indexed in SRS to allow users to query the data within the SRS interface.
true
true
true
true
true
420
4
INTRODUCTION
1
15
[ "b15", "b5", "b16", "b17", "b18" ]
17,202,162
pmid-15961444|pmid-16381856|pmid-14681455|pmid-14681398|pmid-16381875
The new features of InterPro are described in more detail below.
[ "15", "5", "16", "17", "18" ]
64
2,438
0
false
The new features of InterPro are described in more detail below.
[]
The new features of InterPro are described in more detail below.
true
true
true
true
true
420
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
InterPro now integrates protein signatures from 10 different member databases, and links >20 additional resources, including UniProtKB, structural data and specialized protein family databases.
[ "19", "22" ]
193
2,439
0
false
InterPro now integrates protein signatures from 10 different member databases, and links >20 additional resources, including UniProtKB, structural data and specialized protein family databases.
[]
InterPro now integrates protein signatures from 10 different member databases, and links >20 additional resources, including UniProtKB, structural data and specialized protein family databases.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
It has proven its usefulness in the functional characterization of proteins, and is used by genome annotation projects (19–22) and individual researchers worldwide.
[ "19", "22" ]
164
2,440
0
false
It has proven its usefulness in the functional characterization of proteins, and is used by genome annotation projects and individual researchers worldwide.
[ "19–22" ]
It has proven its usefulness in the functional characterization of proteins, and is used by genome annotation projects and individual researchers worldwide.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
In the last year, the InterPro website received ∼3 million hits per month from up to 35 000 unique hosts.
[ "19", "22" ]
105
2,441
0
false
In the last year, the InterPro website received ∼3 million hits per month from up to 35 000 unique hosts.
[]
In the last year, the InterPro website received ∼3 million hits per month from up to 35 000 unique hosts.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
Through the mapping of InterPro entries to GO terms, InterPro contributes the majority of annotations of proteins to GO terms.
[ "19", "22" ]
126
2,442
0
false
Through the mapping of InterPro entries to GO terms, InterPro contributes the majority of annotations of proteins to GO terms.
[]
Through the mapping of InterPro entries to GO terms, InterPro contributes the majority of annotations of proteins to GO terms.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
Approximately 68% of all UniProtKB proteins are annotated with GO terms from a combination of manual annotation and the use of mappings, such as InterPro2GO, Swiss-Prot keyword2GO, etc.
[ "19", "22" ]
185
2,443
0
false
Approximately 68% of all UniProtKB proteins are annotated with GO terms from a combination of manual annotation and the use of mappings, such as InterPro2GO, Swiss-Prot keyword2GO, etc.
[]
Approximately 68% of all UniProtKB proteins are annotated with GO terms from a combination of manual annotation and the use of mappings, such as InterPro2GO, Swiss-Prot keyword2GO, etc.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
InterPro2GO alone provides GO annotations for 61% of UniProtKB proteins, thus accounting for a significant proportion of the total number of annotations currently available.
[ "19", "22" ]
173
2,444
0
false
InterPro2GO alone provides GO annotations for 61% of UniProtKB proteins, thus accounting for a significant proportion of the total number of annotations currently available.
[]
InterPro2GO alone provides GO annotations for 61% of UniProtKB proteins, thus accounting for a significant proportion of the total number of annotations currently available.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
These GO mappings are also available via InterProScan, which facilitates GO annotation to query proteins.
[ "19", "22" ]
105
2,445
0
false
These GO mappings are also available via InterProScan, which facilitates GO annotation to query proteins.
[]
These GO mappings are also available via InterProScan, which facilitates GO annotation to query proteins.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
The current release of InterPro contains more than 13 000 entries, with its signatures covering over 78% of UniProtKB proteins.
[ "19", "22" ]
127
2,446
0
false
The current release of InterPro contains more than 13 000 entries, with its signatures covering over 78% of UniProtKB proteins.
[]
The current release of InterPro contains more than 13 000 entries, with its signatures covering over 78% of UniProtKB proteins.
true
true
true
true
true
421
0
DISCUSSION
1
19
[ "b19", "b22" ]
17,202,162
pmid-15608177|pmid-16381852|pmid-12520033|pmid-15608179|pmid-16381856|pmid-16381859|pmid-12520025|pmid-14681371|pmid-11697912|pmid-16381865|pmid-15608197|pmid-14681407|pmid-16381842|pmid-15980438|pmid-11237011|pmid-10731134
The integration of new protein signatures from the existing and new member databases will continue to increase the coverage, as well as the depth, of InterPro.
[ "19", "22" ]
159
2,447
0
false
The integration of new protein signatures from the existing and new member databases will continue to increase the coverage, as well as the depth, of InterPro.
[]
The integration of new protein signatures from the existing and new member databases will continue to increase the coverage, as well as the depth, of InterPro.
true
true
true
true
true
421
1
DISCUSSION
0
null
null
17,202,162
null
The InterPro database will continue to develop and increase its functionality.
null
78
2,448
0
false
null
null
The InterPro database will continue to develop and increase its functionality.
true
true
true
true
true
422
1
DISCUSSION
0
null
null
17,202,162
null
Future plans include the provision of protein match views for UniParc matches, facilitating the searching and browsing of InterPro entries by function, and the provision of data for unintegrated protein signatures via the InterPro web interface.
null
245
2,449
0
false
null
null
Future plans include the provision of protein match views for UniParc matches, facilitating the searching and browsing of InterPro entries by function, and the provision of data for unintegrated protein signatures via the InterPro web interface.
true
true
true
true
true
422
1
DISCUSSION
0
null
null
17,202,162
null
Integration of signatures into InterPro entries and subsequent annotation of the entries is done manually and is thus of high-quality, but is time-consuming.
null
157
2,450
0
false
null
null
Integration of signatures into InterPro entries and subsequent annotation of the entries is done manually and is thus of high-quality, but is time-consuming.
true
true
true
true
true
422
1
DISCUSSION
0
null
null
17,202,162
null
In order to make the signatures awaiting integration available to the public via the web interface, new entries will be created automatically for the unintegrated signatures and will be searchable by their member database accession numbers.
null
240
2,451
0
false
null
null
In order to make the signatures awaiting integration available to the public via the web interface, new entries will be created automatically for the unintegrated signatures and will be searchable by their member database accession numbers.
true
true
true
true
true
422
1
DISCUSSION
0
null
null
17,202,162
null
The protein matches will be available in the same format as match views from InterPro entries so that the user can see how the new signature relates to existing entries.
null
169
2,452
0
false
null
null
The protein matches will be available in the same format as match views from InterPro entries so that the user can see how the new signature relates to existing entries.
true
true
true
true
true
422
1
DISCUSSION
0
null
null
17,202,162
null
These new features will increase the usefulness of this already popular high-quality resource.
null
94
2,453
0
false
null
null
These new features will increase the usefulness of this already popular high-quality resource.
true
true
true
true
true
422
0
INTRODUCTION
0
null
null
17,135,195
null
The laboratory mouse is one of the most important animal model systems used to study human disease.
null
99
2,454
0
false
null
null
The laboratory mouse is one of the most important animal model systems used to study human disease.
true
true
true
true
true
423
0
INTRODUCTION
0
null
null
17,135,195
null
The well-developed genetic tools (e.g.
null
38
2,455
0
false
null
null
The well-developed genetic tools (e.g.
true
true
true
true
true
423
0
INTRODUCTION
0
null
null
17,135,195
null
targeted and conditional mutations), similar genetics and physiology to humans, a sequenced genome and a large number of established inbred strains provide the underpinnings for analyzing the cause of many disorders.
null
216
2,456
0
false
null
null
targeted and conditional mutations), similar genetics and physiology to humans, a sequenced genome and a large number of established inbred strains provide the underpinnings for analyzing the cause of many disorders.
false
true
true
true
false
423
0
INTRODUCTION
0
null
null
17,135,195
null
Numerous mouse models have been developed to examine the genetics and progress of different syndromes, including many types of cancer.
null
134
2,457
0
false
null
null
Numerous mouse models have been developed to examine the genetics and progress of different syndromes, including many types of cancer.
true
true
true
true
true
423
0
INTRODUCTION
0
null
null
17,135,195
null
A search of PubMed for the terms ‘mouse model’ and ‘cancer’ returns over 2000 publications since 2000, emphasizing the impact of mouse in current cancer research.
null
162
2,458
0
false
null
null
A search of PubMed for the terms ‘mouse model’ and ‘cancer’ returns over 2000 publications since 2000, emphasizing the impact of mouse in current cancer research.
true
true
true
true
true
423
0
INTRODUCTION
0
null
null
17,135,195
null
MTB was established to integrate tumor data obtained from these cancer models and make them available to the scientific community in a robust database that can inform users of existing models, support hypothesis generation, and enable the development of new cancer models.
null
272
2,459
0
false
null
null
MTB was established to integrate tumor data obtained from these cancer models and make them available to the scientific community in a robust database that can inform users of existing models, support hypothesis generation, and enable the development of new cancer models.
true
true
true
true
true
423
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
The Mouse Tumor Biology (MTB) database was first released on the World Wide Web in 1998 (1).
[ "1", "2", "3", "4", "5", "6", "7" ]
92
2,460
1
false
The Mouse Tumor Biology (MTB) database was first released on the World Wide Web in 1998.
[ "1" ]
The Mouse Tumor Biology (MTB) database was first released on the World Wide Web in 1998.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
Data stored in MTB includes incidence and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background, and literature or contributor citations.
[ "1", "2", "3", "4", "5", "6", "7" ]
207
2,461
0
false
Data stored in MTB includes incidence and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background, and literature or contributor citations.
[]
Data stored in MTB includes incidence and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background, and literature or contributor citations.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature.
[ "1", "2", "3", "4", "5", "6", "7" ]
133
2,462
0
false
Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature.
[]
Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
Data can be queried using several web-based query forms centered on the primary data types in MTB: tumor type, mouse strain, genetics, pathology and reference.
[ "1", "2", "3", "4", "5", "6", "7" ]
159
2,463
0
false
Data can be queried using several web-based query forms centered on the primary data types in MTB: tumor type, mouse strain, genetics, pathology and reference.
[]
Data can be queried using several web-based query forms centered on the primary data types in MTB: tumor type, mouse strain, genetics, pathology and reference.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
Users specify one or more parameters to retrieve a Results Summary Page listing all MTB entries that satisfy the query parameters.
[ "1", "2", "3", "4", "5", "6", "7" ]
130
2,464
0
false
Users specify one or more parameters to retrieve a Results Summary Page listing all MTB entries that satisfy the query parameters.
[]
Users specify one or more parameters to retrieve a Results Summary Page listing all MTB entries that satisfy the query parameters.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
An advanced search form combines features of the strain, genetics, pathology and tumor search forms, allowing users to ask complex questions.
[ "1", "2", "3", "4", "5", "6", "7" ]
141
2,465
0
false
An advanced search form combines features of the strain, genetics, pathology and tumor search forms, allowing users to ask complex questions.
[]
An advanced search form combines features of the strain, genetics, pathology and tumor search forms, allowing users to ask complex questions.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
MTB is updated weekly with data obtained from curation of the primary literature and from direct database submissions from researchers.
[ "1", "2", "3", "4", "5", "6", "7" ]
135
2,466
0
false
MTB is updated weekly with data obtained from curation of the primary literature and from direct database submissions from researchers.
[]
MTB is updated weekly with data obtained from curation of the primary literature and from direct database submissions from researchers.
true
true
true
true
true
424
1
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
MTB is accessible from the Mouse Genome Informatics website (MGI) and shares database infrastructure and standard gene nomenclature with the Mouse Genome Database (MGD) (2) and the Gene Expression Database (GXD) (3).
[ "1", "2", "3", "4", "5", "6", "7" ]
216
2,467
1
false
MTB is accessible from the Mouse Genome Informatics website (MGI) and shares database infrastructure and standard gene nomenclature with the Mouse Genome Database (MGD) and the Gene Expression Database (GXD).
[ "2", "3" ]
MTB is accessible from the Mouse Genome Informatics website (MGI) and shares database infrastructure and standard gene nomenclature with the Mouse Genome Database (MGD) and the Gene Expression Database (GXD).
true
true
true
true
true
424
1
INTRODUCTION
1
4
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
MTB also provides links to other related onlineresources such as the Mouse Phenome Database (MPD) (4), the Biology of the Mammary Gland website (), Festing's Listing of Inbred Strains of Mice (5), the JAX® Mice website (), the Mammary Cancer in Humans and Mice: A Tutorial for Comparative Pathology: The CD-ROM Web site ...
[ "1", "2", "3", "4", "5", "6", "7" ]
407
2,468
1
false
MTB also provides links to other related onlineresources such as the Mouse Phenome Database (MPD), the Biology of the Mammary Gland website (), Festing's Listing of Inbred Strains of Mice, the JAX® Mice website (), the Mammary Cancer in Humans and Mice: A Tutorial for Comparative Pathology: The CD-ROM Web site, and the...
[ "4", "5", "6", "7" ]
MTB also provides links to other related onlineresources such as the Mouse Phenome Database (MPD), the Biology of the Mammary Gland website (), Festing's Listing of Inbred Strains of Mice, the JAX® Mice website (), the Mammary Cancer in Humans and Mice: A Tutorial for Comparative Pathology: The CD-ROM Web site, and the...
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
Links to additional resources, such as Ensembl, are accessed using reference links to MGI and the associated gene detail pages.
[ "1", "2", "3", "4", "5", "6", "7" ]
127
2,469
0
false
Links to additional resources, such as Ensembl, are accessed using reference links to MGI and the associated gene detail pages.
[]
Links to additional resources, such as Ensembl, are accessed using reference links to MGI and the associated gene detail pages.
true
true
true
true
true
424
1
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,135,195
pmid-9847151|pmid-16381933|pmid-11125060|pmid-15130929|pmid-10615122|pmid-11467469|pmid-14728559
Direct submission of mouse tumor data and pathology images from the cancer research community is encouraged and MTB has developed a web-based system to facilitate entry of these data.
[ "1", "2", "3", "4", "5", "6", "7" ]
183
2,470
0
false
Direct submission of mouse tumor data and pathology images from the cancer research community is encouraged and MTB has developed a web-based system to facilitate entry of these data.
[]
Direct submission of mouse tumor data and pathology images from the cancer research community is encouraged and MTB has developed a web-based system to facilitate entry of these data.
true
true
true
true
true
424
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
Human tissue-specific genes were reported to be longer than housekeeping genes, both in coding and intronic parts.
[ "1", "11" ]
114
2,471
0
false
Human tissue-specific genes were reported to be longer than housekeeping genes, both in coding and intronic parts.
[]
Human tissue-specific genes were reported to be longer than housekeeping genes, both in coding and intronic parts.
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The competing models were proposed to explain this observation: selection for economy (in housekeeping genes), mutation bias and ‘genome design’ (i.e.
[ "1", "11" ]
150
2,472
0
false
The competing models were proposed to explain this observation: selection for economy (in housekeeping genes), mutation bias and ‘genome design’ (i.e.
[]
The competing models were proposed to explain this observation: selection for economy (in housekeeping genes), mutation bias and ‘genome design’ (i.e.
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
functional complexity) (1–11).
[ "1", "11" ]
30
2,473
0
false
functional complexity).
[ "1–11" ]
functional complexity).
false
true
true
true
false
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The first two models assume a neutralist (permissive) interpretation of the accumulation of DNA in eukaryotic genomes.
[ "1", "11" ]
118
2,474
0
false
The first two models assume a neutralist (permissive) interpretation of the accumulation of DNA in eukaryotic genomes.
[]
The first two models assume a neutralist (permissive) interpretation of the accumulation of DNA in eukaryotic genomes.
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
In contrast, the ‘genome design’ model suggests that the length of genomic elements is mostly determined by their functional load.
[ "1", "11" ]
130
2,475
0
false
In contrast, the ‘genome design’ model suggests that the length of genomic elements is mostly determined by their functional load.
[]
In contrast, the ‘genome design’ model suggests that the length of genomic elements is mostly determined by their functional load.
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
In particular, the greater amount of intra- and intergenic noncoding DNA, in which the tissue-specific genes are embedded, may be involved in the more complex regulation and chromatin-mediated suppression of these genes, whereas the greater length of coding sequences may be related to more complex protein functional ar...
[ "1", "11" ]
332
2,476
0
false
In particular, the greater amount of intra- and intergenic noncoding DNA, in which the tissue-specific genes are embedded, may be involved in the more complex regulation and chromatin-mediated suppression of these genes, whereas the greater length of coding sequences may be related to more complex protein functional ar...
[]
In particular, the greater amount of intra- and intergenic noncoding DNA, in which the tissue-specific genes are embedded, may be involved in the more complex regulation and chromatin-mediated suppression of these genes, whereas the greater length of coding sequences may be related to more complex protein functional ar...
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
From the standpoint of information theory, the regulation of intermediately expressed genes should be most complex (Figure 1).
[ "1", "11" ]
126
2,477
0
false
From the standpoint of information theory, the regulation of intermediately expressed genes should be most complex.
[ "Figure 1" ]
From the standpoint of information theory, the regulation of intermediately expressed genes should be most complex.
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
Here, I test this suggestion and investigate in the genomewide context both the length (using the updated databases and a finer expression breadth scale) and the informational load (using a novel approach) of human genes with different expression pattern.
[ "1", "11" ]
255
2,478
0
false
Here, I test this suggestion and investigate in the genomewide context both the length (using the updated databases and a finer expression breadth scale) and the informational load (using a novel approach) of human genes with different expression pattern.
[]
Here, I test this suggestion and investigate in the genomewide context both the length (using the updated databases and a finer expression breadth scale) and the informational load (using a novel approach) of human genes with different expression pattern.
true
true
true
true
true
425
0
INTRODUCTION
1
1
[ "b1", "b11" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The informational load is extensively studied on all available levels: from gene participation in protein interaction networks, pathways and modules reflected in Gene Ontology categories through transcription factor regulatory sets and protein functional domains to amino acid tuples (words of fixed size) in encoded pro...
[ "1", "11" ]
380
2,479
0
false
The informational load is extensively studied on all available levels: from gene participation in protein interaction networks, pathways and modules reflected in Gene Ontology categories through transcription factor regulatory sets and protein functional domains to amino acid tuples (words of fixed size) in encoded pro...
[]
The informational load is extensively studied on all available levels: from gene participation in protein interaction networks, pathways and modules reflected in Gene Ontology categories through transcription factor regulatory sets and protein functional domains to amino acid tuples (words of fixed size) in encoded pro...
true
true
true
true
true
425
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The whole picture can be summarized as follows.
[ "34", "35", "36", "37", "38" ]
47
2,480
0
false
The whole picture can be summarized as follows.
[]
The whole picture can be summarized as follows.
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
It was argued that the overtaking growth of the number of genes coding for transcription factors over the total number of genes limited the growth of prokaryotic genomes (34).
[ "34", "35", "36", "37", "38" ]
175
2,481
1
false
It was argued that the overtaking growth of the number of genes coding for transcription factors over the total number of genes limited the growth of prokaryotic genomes.
[ "34" ]
It was argued that the overtaking growth of the number of genes coding for transcription factors over the total number of genes limited the growth of prokaryotic genomes.
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The problem of regulatory complexity turns out to be even more severe for the eukaryotic genomes (35,36).
[ "34", "35", "36", "37", "38" ]
105
2,482
0
false
The problem of regulatory complexity turns out to be even more severe for the eukaryotic genomes.
[ "35,36" ]
The problem of regulatory complexity turns out to be even more severe for the eukaryotic genomes.
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The most complex regulatory problems should appear in the case of intermediately expressed genes (Figure 1).
[ "34", "35", "36", "37", "38" ]
108
2,483
0
false
The most complex regulatory problems should appear in the case of intermediately expressed genes (Figure 1).
[]
The most complex regulatory problems should appear in the case of intermediately expressed genes (Figure 1).
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
Therefore, the burden of regulatory complexity might force the dichotomy of housekeeping versus tissue-specific genes in the multicellular organisms [which can be seen in the histogram of genes expressed in different numbers of tissues: e.g.
[ "34", "35", "36", "37", "38" ]
241
2,484
0
false
Therefore, the burden of regulatory complexity might force the dichotomy of housekeeping versus tissue-specific genes in the multicellular organisms [which can be seen in the histogram of genes expressed in different numbers of tissues: e.g.
[]
Therefore, the burden of regulatory complexity might force the dichotomy of housekeeping versus tissue-specific genes in the multicellular organisms [which can be seen in the histogram of genes expressed in different numbers of tissues: e.g.
true
true
true
true
true
426
0
DISCUSSION
1
37
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
figure 1 in (37); figure 2 in (38)].
[ "34", "35", "36", "37", "38" ]
36
2,485
1
false
figure 1 in ; figure 2 in ].
[ "37", "38" ]
figure 1 in ; figure 2 in ].
false
true
true
true
false
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The occurrence of protein functional domains, participation in transcription factor regulatory sets, pathways, protein interactions, biological processes, molecular functions and cellular components also reflect this dichotomy, showing the maximum genomewide-contextual uncertainty (and thus, informational load) in the ...
[ "34", "35", "36", "37", "38" ]
351
2,486
0
false
The occurrence of protein functional domains, participation in transcription factor regulatory sets, pathways, protein interactions, biological processes, molecular functions and cellular components also reflect this dichotomy, showing the maximum genomewide-contextual uncertainty (and thus, informational load) in the ...
[]
The occurrence of protein functional domains, participation in transcription factor regulatory sets, pathways, protein interactions, biological processes, molecular functions and cellular components also reflect this dichotomy, showing the maximum genomewide-contextual uncertainty (and thus, informational load) in the ...
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
In other words, there are much less intermediate-specific modules (if any) than housekeeping and tissue-specific modules (Tables 1 and 2).
[ "34", "35", "36", "37", "38" ]
138
2,487
0
false
In other words, there are much less intermediate-specific modules (if any) than housekeeping and tissue-specific modules (Tables 1 and 2).
[]
In other words, there are much less intermediate-specific modules (if any) than housekeeping and tissue-specific modules (Tables 1 and 2).
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
This effect is observed notwithstanding the fact that gene expression bins are normalized to the roughly equal numbers of genes.
[ "34", "35", "36", "37", "38" ]
128
2,488
0
false
This effect is observed notwithstanding the fact that gene expression bins are normalized to the roughly equal numbers of genes.
[]
This effect is observed notwithstanding the fact that gene expression bins are normalized to the roughly equal numbers of genes.
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
Thus, the dichotomy of housekeeping versus tissue-specific entities is much more pronounced on the modular level than on the molecular level.
[ "34", "35", "36", "37", "38" ]
141
2,489
0
false
Thus, the dichotomy of housekeeping versus tissue-specific entities is much more pronounced on the modular level than on the molecular level.
[]
Thus, the dichotomy of housekeeping versus tissue-specific entities is much more pronounced on the modular level than on the molecular level.
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
The intermediately expressed genes possibly connect housekeeping and tissue-specific modules.
[ "34", "35", "36", "37", "38" ]
93
2,490
0
false
The intermediately expressed genes possibly connect housekeeping and tissue-specific modules.
[]
The intermediately expressed genes possibly connect housekeeping and tissue-specific modules.
true
true
true
true
true
426
0
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,062,620
pmid-12134150|pmid-16461636|pmid-15705831|pmid-11233450|pmid-11360989|pmid-12930973|pmid-15998913
In any case, they have the higher functional and regulatory complexity reflected in their greater length, which is consistent with the ‘genome design’ model.
[ "34", "35", "36", "37", "38" ]
157
2,491
0
false
In any case, they have the higher functional and regulatory complexity reflected in their greater length, which is consistent with the ‘genome design’ model.
[]
In any case, they have the higher functional and regulatory complexity reflected in their greater length, which is consistent with the ‘genome design’ model.
true
true
true
true
true
426
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
The domain architecture is considered the most important level of protein functional complexity, especially in the eukaryotic genomes (39–41).
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
142
2,492
0
false
The domain architecture is considered the most important level of protein functional complexity, especially in the eukaryotic genomes.
[ "39–41" ]
The domain architecture is considered the most important level of protein functional complexity, especially in the eukaryotic genomes.
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
Proteins encoded by the intermediately expressed genes are shown here to consist of a greater number of various domains and therefore may perform more complex and diverse functions.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
181
2,493
0
false
Proteins encoded by the intermediately expressed genes are shown here to consist of a greater number of various domains and therefore may perform more complex and diverse functions.
[]
Proteins encoded by the intermediately expressed genes are shown here to consist of a greater number of various domains and therefore may perform more complex and diverse functions.
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
The higher complexity of the intermediately expressed genes is also reflected in the frequency of amino acid tuples in encoded proteins and nucleotide tuples in introns and promoter regions.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
190
2,494
0
false
The higher complexity of the intermediately expressed genes is also reflected in the frequency of amino acid tuples in encoded proteins and nucleotide tuples in introns and promoter regions.
[]
The higher complexity of the intermediately expressed genes is also reflected in the frequency of amino acid tuples in encoded proteins and nucleotide tuples in introns and promoter regions.
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
A possible functional load of introns is discussed in (11,42–47).
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
65
2,495
0
false
A possible functional load of introns is discussed in.
[ "11,42–47" ]
A possible functional load of introns is discussed in.
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
Briefly, introns can harbor a plethora of regulatory elements acting in multiple ways: the interaction with transcription factors (as enhancers and suppressors), the regulation mediated by splicing, and the action of noncoding RNAs located in introns (to say nothing of alternative splicing which alters the protein stru...
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
327
2,496
0
false
Briefly, introns can harbor a plethora of regulatory elements acting in multiple ways: the interaction with transcription factors (as enhancers and suppressors), the regulation mediated by splicing, and the action of noncoding RNAs located in introns (to say nothing of alternative splicing which alters the protein stru...
[]
Briefly, introns can harbor a plethora of regulatory elements acting in multiple ways: the interaction with transcription factors (as enhancers and suppressors), the regulation mediated by splicing, and the action of noncoding RNAs located in introns (to say nothing of alternative splicing which alters the protein stru...
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
It is noteworthy that first intron, which is more often known to contain regulatory elements (48,49), is longer in the intermediately expressed genes (Supplementary Figure 7).
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
175
2,497
0
false
It is noteworthy that first intron, which is more often known to contain regulatory elements, is longer in the intermediately expressed genes (Supplementary Figure 7).
[ "48,49" ]
It is noteworthy that first intron, which is more often known to contain regulatory elements, is longer in the intermediately expressed genes (Supplementary Figure 7).
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
The situation is further complicated by participation of introns in chromatin organization and interplay of the latter with transcriptional regulation (e.g.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
156
2,498
0
false
The situation is further complicated by participation of introns in chromatin organization and interplay of the latter with transcriptional regulation (e.g.
[]
The situation is further complicated by participation of introns in chromatin organization and interplay of the latter with transcriptional regulation (e.g.
true
true
true
true
true
427
1
DISCUSSION
1
51
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
It is interesting that in the yeast, introns are longer in the highly expressed genes (51), which contradicts the ‘selection for economy’ model.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
144
2,499
1
false
It is interesting that in the yeast, introns are longer in the highly expressed genes, which contradicts the ‘selection for economy’ model.
[ "51" ]
It is interesting that in the yeast, introns are longer in the highly expressed genes, which contradicts the ‘selection for economy’ model.
true
true
true
true
true
427