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{{Coexpression_clusters
{
|full_id=C678_Smooth_CD14_embryonic_mesothelioma_gall_Fibroblast_meningioma
|

Latest revision as of 11:28, 17 September 2013


Full id: C678_Smooth_CD14_embryonic_mesothelioma_gall_Fibroblast_meningioma



Phase1 CAGE Peaks

Hg19::chr10:91152368..91152419,+p1@IFIT1
Hg19::chr12:113344811..113344832,+p2@OAS1
Hg19::chr12:113405759..113405764,+p@chr12:113405759..113405764
+
Hg19::chr17:40263911..40263923,-p6@DHX58
Hg19::chr1:948866..948885,+p1@ISG15
Hg19::chr22:18632907..18632918,+p3@USP18
Hg19::chr22:18632929..18632945,+p1@USP18
Hg19::chr2:7005572..7005619,-p2@CMPK2
Hg19::chr4:89299964..89299986,+p3@HERC6
Hg19::chr4:89299994..89300011,+p2@HERC6
Hg19::chr4:89300057..89300068,+p7@HERC6
Hg19::chr4:89300072..89300089,+p4@HERC6


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
0.0001270572211922370.0268090736715619271RIG-I-like receptor signaling pathway (KEGG):04622
6.27877433870237e-050.019872320781993250Type II interferon signaling (IFNG) (Wikipathways):WP619
3.67536037054371e-082.32650311455417e-055511Signaling in Immune system (Reactome):REACT_6900



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:0006512ubiquitin cycle0.00539557078421984
GO:0009615response to virus0.00539557078421984
GO:0032020ISG15-protein conjugation0.0105553619861631
GO:0051707response to other organism0.0105553619861631
GO:0043632modification-dependent macromolecule catabolic process0.0105553619861631
GO:0019941modification-dependent protein catabolic process0.0105553619861631
GO:0009607response to biotic stimulus0.0105553619861631
GO:0051603proteolysis involved in cellular protein catabolic process0.0105553619861631
GO:0044257cellular protein catabolic process0.0105553619861631
GO:0051704multi-organism process0.012320234401282
GO:0030163protein catabolic process0.0127801185248416
GO:0005737cytoplasm0.017462333649797
GO:0043285biopolymer catabolic process0.017462333649797
GO:0044424intracellular part0.0193439322321757
GO:0044265cellular macromolecule catabolic process0.01998048690809
GO:0009057macromolecule catabolic process0.0253150277329111
GO:0043687post-translational protein modification0.0253150277329111
GO:0005622intracellular0.0348662193231298
GO:0044248cellular catabolic process0.0368921277854879
GO:0006464protein modification process0.0368921277854879
GO:0043412biopolymer modification0.0393377907931135
GO:0009056catabolic process0.0439058078389735
GO:0003723RNA binding0.0439058078389735



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
hemolymphoid system1.77e-13108
hematopoietic system2.49e-1398
blood island2.49e-1398
adult organism1.86e-12114
immune system4.30e-1193
bone marrow3.00e-0976
bone element1.92e-0882
skeletal element3.77e-0790


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)
MA0003.12.22856
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.455267
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.90675
MA0050.18.56285
MA0051.19.83172
MA0052.10.682867
MA0055.10.400018
MA0056.10
MA0057.10.147728
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.605357
MA0063.10
MA0066.11.0654
MA0067.11.06751
MA0068.10.8463
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.0284577
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0178242
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.11.4437
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.535462
MA0105.10.130274
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.13.46301
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.567946
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.39221
MA0145.11.05522
MA0146.10.00710499
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.981089
MA0039.20.431698
MA0138.20.503176
MA0002.20.316618
MA0137.20.595725
MA0104.20.102626
MA0047.20.440861
MA0112.20.216805
MA0065.20.733267
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.12.20313
MA0155.10.392911
MA0156.11.13151
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.00310762
MA0163.10.0369192
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.0178219
MA0102.21.28978
MA0258.10.375
MA0259.10.455773
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
E2F1#186972.862643708679610.004360763229147680.0206733432087587
GATA1#262355.650128393250180.001110393113343090.00771168681769114
HNF4A#317235.783072590738420.01324395628490540.0468527047774283
IRF1#365953.182151563984960.01370188570770830.0483368093709625
MEF2A#420546.247743636548020.002834712427412020.0153714709868372
NFKB1#479062.744031712096920.01234247201454430.044716253329413
PAX5#507973.890579893187070.0006699722807011360.0054094499438845
POLR2A#5430101.789544313798390.01056859658770230.0390508989571215
SMC3#912645.014977614977610.006261783977021150.027627664939213
STAT1#6772610.35329374859969.08847659828404e-060.000242759950754012
STAT2#6773632.63188559322031.09905339974521e-088.26378963398058e-07
TCF12#693854.431027042577680.003302501388921610.0170832066645658
TFAP2C#702276.30538335575183.01291531004594e-050.000619787004266079
ZNF143#770244.500292184075970.009180626966575010.0347245943706406



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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