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Coexpression cluster:C1671: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.24383,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;3.07977,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;3.05902,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;1.55172,MA0061.1;0.791444,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.692739,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.0140295,MA0074.1;0.730989,MA0076.1;3.37477,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;1.99092,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;1.35428,MA0147.1;1.00307,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;3.94248,MA0035.2;0.691506,MA0039.2;1.92202,MA0138.2;1.95446,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.813062,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.23503,MA0163.1;1.05321,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;1.03616,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.80881,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1671_Alveolar_Mesenchymal_Renal_Pericytes_Fibroblast_Placental_Smooth



Phase1 CAGE Peaks

Hg19::chr12:49961883..49961933,-p1@MCRS1
Hg19::chr17:80009748..80009808,+p1@GPS1
Hg19::chr19:52693259..52693335,+p1@PPP2R1A
Hg19::chr8:144911476..144911517,-p1@PUF60
Hg19::chr9:131873659..131873703,+p1@PPP2R4


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
0.000118258313708250.0249525041924409299IL-6 Signaling Pathway (Wikipathways):WP364
0.000118258313708250.0249525041924409299Wnt Signaling Pathway and Pluripotency (Wikipathways):WP399
1.54262472139839e-050.00976481448645182236Glycogen Metabolism (Wikipathways):WP500



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0043086negative regulation of catalytic activity3.78194462493104e-05
GO:0045936negative regulation of phosphate metabolic process0.000158051900403208
GO:0000188inactivation of MAPK activity0.000206622407020211
GO:0043407negative regulation of MAP kinase activity0.000279449198969006
GO:0000159protein phosphatase type 2A complex0.000401363718236737
GO:0008601protein phosphatase type 2A regulator activity0.000401363718236737
GO:0008287protein serine/threonine phosphatase complex0.000691525695820129
GO:0006469negative regulation of protein kinase activity0.000691525695820129
GO:0033673negative regulation of kinase activity0.000691525695820129
GO:0051348negative regulation of transferase activity0.000691525695820129
GO:0051174regulation of phosphorus metabolic process0.000789676369929298
GO:0019220regulation of phosphate metabolic process0.000789676369929298
GO:0019888protein phosphatase regulator activity0.000893608372889712
GO:0050790regulation of catalytic activity0.000893608372889712
GO:0019208phosphatase regulator activity0.000893608372889712
GO:0043405regulation of MAP kinase activity0.00102509877655625
GO:0065009regulation of a molecular function0.00102509877655625
GO:0051248negative regulation of protein metabolic process0.00115829653005875
GO:0046982protein heterodimerization activity0.00115829653005875
GO:0032516positive regulation of phosphoprotein phosphatase activity0.00149739683319767
GO:0035305negative regulation of dephosphorylation0.00149739683319767
GO:0035308negative regulation of protein amino acid dephosphorylation0.00149739683319767
GO:0032515negative regulation of phosphoprotein phosphatase activity0.00149739683319767
GO:0000165MAPKKK cascade0.00187182064475157
GO:0043234protein complex0.00225849552721242
GO:0008160protein tyrosine phosphatase activator activity0.00237504134788093
GO:0035304regulation of protein amino acid dephosphorylation0.00237504134788093
GO:0035306positive regulation of dephosphorylation0.00237504134788093
GO:0035307positive regulation of protein amino acid dephosphorylation0.00237504134788093
GO:0044428nuclear part0.00256907040405961
GO:0008380RNA splicing0.00322838175416037
GO:0051004regulation of lipoprotein lipase activity0.00322838175416037
GO:0005625soluble fraction0.00328201699106695
GO:0045859regulation of protein kinase activity0.00328201699106695
GO:0043549regulation of kinase activity0.00328201699106695
GO:0006470protein amino acid dephosphorylation0.00328201699106695
GO:0051338regulation of transferase activity0.00328201699106695
GO:0051721protein phosphatase 2A binding0.00335941899159541
GO:0050732negative regulation of peptidyl-tyrosine phosphorylation0.00335941899159541
GO:0042518negative regulation of tyrosine phosphorylation of Stat3 protein0.00335941899159541
GO:0042532negative regulation of tyrosine phosphorylation of STAT protein0.00335941899159541
GO:0016311dephosphorylation0.00371002105991095
GO:0046426negative regulation of JAK-STAT cascade0.00391272925030626
GO:0035303regulation of dephosphorylation0.00391272925030626
GO:0032991macromolecular complex0.00402677508269199
GO:0051346negative regulation of hydrolase activity0.00439531790564664
GO:0019907cyclin-dependent protein kinase activating kinase holoenzyme complex0.00439531790564664
GO:0046983protein dimerization activity0.00537789962602607
GO:0033239negative regulation of amine metabolic process0.00537789962602607
GO:0001933negative regulation of protein amino acid phosphorylation0.00537789962602607
GO:0045763negative regulation of amino acid metabolic process0.00537789962602607
GO:0007243protein kinase cascade0.00537789962602607
GO:0031324negative regulation of cellular metabolic process0.00541627948881933
GO:0005515protein binding0.0055324140350824
GO:0008180signalosome0.0055324140350824
GO:0042516regulation of tyrosine phosphorylation of Stat3 protein0.0055324140350824
GO:0042503tyrosine phosphorylation of Stat3 protein0.0059348073943482
GO:0005095GTPase inhibitor activity0.0059348073943482
GO:0051246regulation of protein metabolic process0.00595602286000441
GO:0009892negative regulation of metabolic process0.00610674870586535
GO:0043666regulation of phosphoprotein phosphatase activity0.00610674870586535
GO:0019211phosphatase activator activity0.00610674870586535
GO:0042326negative regulation of phosphorylation0.00655577712693528
GO:0042509regulation of tyrosine phosphorylation of STAT protein0.00699071010828025
GO:0046425regulation of JAK-STAT cascade0.00794117338964218
GO:0006396RNA processing0.00819423571368854
GO:0019903protein phosphatase binding0.00873031183308974
GO:0007260tyrosine phosphorylation of STAT protein0.00910738425907021
GO:0019902phosphatase binding0.0109673418675596
GO:0045937positive regulation of phosphate metabolic process0.0122826775851395
GO:0030111regulation of Wnt receptor signaling pathway0.0130769167866152
GO:0006275regulation of DNA replication0.0131889294960938
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0131889294960938
GO:0005634nucleus0.0136970240374491
GO:0006464protein modification process0.0139019635560335
GO:0006672ceramide metabolic process0.0144746637695659
GO:0043412biopolymer modification0.0151993344077791
GO:0046519sphingoid metabolic process0.0154229990596633
GO:0007259JAK-STAT cascade0.0169640923904088
GO:0006915apoptosis0.0175839219603667
GO:0012501programmed cell death0.0175839219603667
GO:0018108peptidyl-tyrosine phosphorylation0.0175839219603667
GO:0018212peptidyl-tyrosine modification0.0175839219603667
GO:0065007biological regulation0.0175839219603667
GO:0001932regulation of protein amino acid phosphorylation0.0175839219603667
GO:0000267cell fraction0.0175839219603667
GO:0033238regulation of amine metabolic process0.0175839219603667
GO:0006521regulation of amino acid metabolic process0.0175839219603667
GO:0008219cell death0.0175839219603667
GO:0016265death0.0175839219603667
GO:0051052regulation of DNA metabolic process0.0184923501563252
GO:0048522positive regulation of cellular process0.0189376544774643
GO:0030308negative regulation of cell growth0.0195671720898842
GO:0045792negative regulation of cell size0.0197231137967106
GO:0044424intracellular part0.0198778405874726
GO:0045926negative regulation of growth0.0218066619643468
GO:0010033response to organic substance0.0218919223482464
GO:0048518positive regulation of biological process0.0218919223482464
GO:0042325regulation of phosphorylation0.0221818958115347
GO:0007254JNK cascade0.0223018899835282
GO:0030155regulation of cell adhesion0.0224194681089413
GO:0031098stress-activated protein kinase signaling pathway0.0226476577150369
GO:0006665sphingolipid metabolic process0.0226476577150369
GO:0048523negative regulation of cellular process0.0235410929670742
GO:0051345positive regulation of hydrolase activity0.0248182608014528
GO:0048519negative regulation of biological process0.0248950097654811
GO:0043283biopolymer metabolic process0.0265148531260851
GO:0048468cell development0.0267244856626852
GO:0051247positive regulation of protein metabolic process0.0267244856626852
GO:0031323regulation of cellular metabolic process0.0275270140054957
GO:0044446intracellular organelle part0.0310106326982573
GO:0044422organelle part0.0310106326982573
GO:0019222regulation of metabolic process0.0311549359038064
GO:0009968negative regulation of signal transduction0.0312291095401296
GO:0005622intracellular0.0330791608794974
GO:0018193peptidyl-amino acid modification0.0356717009529934
GO:0043231intracellular membrane-bound organelle0.0357841435503027
GO:0043227membrane-bound organelle0.0357841435503027
GO:0045595regulation of cell differentiation0.0412638299707287
GO:0016055Wnt receptor signaling pathway0.0412638299707287
GO:0006793phosphorus metabolic process0.0432363809675238
GO:0006796phosphate metabolic process0.0432363809675238
GO:0042803protein homodimerization activity0.0438331172398033
GO:0001558regulation of cell growth0.0445698769321459
GO:0006261DNA-dependent DNA replication0.0450241300018458
GO:0048869cellular developmental process0.0469299736103358
GO:0030154cell differentiation0.0469299736103358
GO:0003823antigen binding0.0471333021701575



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle3.58e-1878
cell layer9.11e-17309
epithelium6.00e-16306
vasculature4.35e-1578
vascular system4.35e-1578
paraxial mesoderm5.34e-1572
presumptive paraxial mesoderm5.34e-1572
somite6.46e-1571
presomitic mesoderm6.46e-1571
presumptive segmental plate6.46e-1571
dermomyotome6.46e-1571
trunk paraxial mesoderm6.46e-1571
dense mesenchyme tissue7.22e-1573
multilaminar epithelium3.47e-1483
epithelial tube8.55e-14117
unilaminar epithelium1.84e-13148
splanchnic layer of lateral plate mesoderm2.81e-1383
artery5.81e-1342
arterial blood vessel5.81e-1342
arterial system5.81e-1342
skeletal muscle tissue1.45e-1262
striated muscle tissue1.45e-1262
myotome1.45e-1262
vessel4.98e-1268
epithelial tube open at both ends6.38e-1259
blood vessel6.38e-1259
blood vasculature6.38e-1259
vascular cord6.38e-1259
muscle tissue1.83e-1164
musculature1.83e-1164
musculature of body1.83e-1164
circulatory system4.80e-11112
anatomical cluster5.31e-11373
cardiovascular system2.22e-10109
multi-tissue structure2.56e-10342
mesenchyme9.30e-10160
entire embryonic mesenchyme9.30e-10160
trunk mesenchyme2.66e-09122
systemic artery3.16e-0933
systemic arterial system3.16e-0933
nephron epithelium2.22e-0815
renal tubule2.22e-0815
nephron tubule2.22e-0815
nephron2.22e-0815
uriniferous tubule2.22e-0815
nephrogenic mesenchyme2.22e-0815
trunk2.90e-08199
tube7.49e-08192
organism subdivision1.14e-07264
parenchyma1.33e-0715
excretory tube1.67e-0716
kidney epithelium1.67e-0716
cortex of kidney4.64e-0712
renal parenchyma4.64e-0712


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.24383
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.13.07977
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.13.05902
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.13.37477
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.11.99092
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.35428
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.23.94248
MA0035.20.691506
MA0039.21.92202
MA0138.21.95446
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.23503
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.03616
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL3#602213.81884112149530.007902823332280840.0324358628468159
E2F1#186943.925911371903460.007214984547106360.0298686289485984
EGR1#195843.990543275848110.0067800983001440.0287602731964071
ELF1#199754.258097958807540.0007142416939776840.00572659974492057
ETS1#211359.728760922202341.14685159850452e-050.00029213666852735
GABPB1#255345.654147068945740.001776696502096670.0109054602399338
HEY1#2346254.040111043105710.0009288852205177990.00673693357955961
IRF1#365946.109731002851120.001315525264767990.00880718866199388
MXI1#460135.976942977255580.008653004889366880.0329448863563336
MYC#460944.177825497287520.005691969036823440.0256721175607533
NFKB1#479044.390450739355070.004707732692524960.0221963294963936
NR2C2#7182213.04584436209630.00883636412768260.0335463843377333
NRF1#489937.326167668626540.004839689817117540.022685353656027
POU2F2#545235.463674434645510.01115650094469780.0410055886737036
REST#597847.720022972902420.0005286363773650570.00457189918976724
SIN3A#2594255.408884726815140.0002159522671657270.00247789923429151
SIX5#147912413.66937228436725.58844770365977e-050.000937292259069411
SP1#666744.558705102512720.00407573565781680.0194768133775671
SP2#6668210.46141219753790.01353191183347140.0477742999112946
TAF1#687253.343046285745290.002394600090870310.0135198204611528
TAF7#687949.146455523939130.0002720662872412990.00290238314332932
TCF12#693836.380678941311850.007185168653258840.029825589387031
THAP1#55145212.54765784114050.009528434667386530.0358880662204617
YY1#752843.928936599883080.007193866269917620.0298344200200106
ZEB1#6935413.51074561403515.85221769500384e-050.00096693523785557



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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