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Coexpression cluster:C226

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Full id: C226_Corneal_Keratinocyte_Esophageal_Urothelial_Mammary_Bronchial_Tracheal



Phase1 CAGE Peaks

Hg19::chr11:120008848..120008862,-p4@TRIM29
Hg19::chr11:66673490..66673527,-p@chr11:66673490..66673527
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Hg19::chr11:66673538..66673570,-p@chr11:66673538..66673570
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Hg19::chr11:72432950..72432974,-p9@ARAP1
Hg19::chr12:120105914..120105973,+p2@PRKAB1
Hg19::chr12:52887143..52887158,-p8@KRT6A
Hg19::chr12:52887160..52887186,-p3@KRT6A
Hg19::chr16:68679173..68679184,+p2@CDH3
Hg19::chr16:68679193..68679253,+p1@CDH3
Hg19::chr16:68679261..68679268,+p3@CDH3
Hg19::chr16:68716248..68716260,-p@chr16:68716248..68716260
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Hg19::chr17:39925803..39925824,-p@chr17:39925803..39925824
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Hg19::chr17:39942208..39942219,-p7@JUP
Hg19::chr17:39942220..39942242,-p2@JUP
Hg19::chr17:39942245..39942256,-p9@JUP
Hg19::chr17:39942268..39942282,-p6@JUP
Hg19::chr17:39942286..39942313,-p3@JUP
Hg19::chr17:39942940..39942970,-p1@JUP
Hg19::chr17:73717531..73717550,+p2@ITGB4
Hg19::chr17:73717551..73717609,+p1@ITGB4
Hg19::chr17:73717624..73717635,+p3@ITGB4
Hg19::chr17:7493405..7493419,-p1@SOX15
Hg19::chr17:8006982..8007017,-p@chr17:8006982..8007017
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Hg19::chr1:153585571..153585629,-p2@S100A16
Hg19::chr1:153585634..153585651,-p7@S100A16
Hg19::chr1:153588789..153588808,-p1@S100A14
Hg19::chr1:200864020..200864063,+p1@C1orf106
Hg19::chr1:200864071..200864088,+p3@C1orf106
Hg19::chr1:201368430..201368460,-p1@LAD1
Hg19::chr1:201368476..201368498,-p4@LAD1
Hg19::chr1:207206059..207206084,-p3@C1orf116
Hg19::chr1:209825762..209825779,-p1@LAMB3
Hg19::chr1:209825932..209825936,-p10@LAMB3
Hg19::chr1:209826381..209826392,-p@chr1:209826381..209826392
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Hg19::chr1:209979411..209979433,-p2@IRF6
Hg19::chr1:209979449..209979460,-p3@IRF6
Hg19::chr1:27189631..27189648,+p1@SFN
Hg19::chr1:27190343..27190365,-p4@uc010ofi.1
Hg19::chr1:27190373..27190427,-p1@uc010ofi.1
Hg19::chr1:27190643..27190678,-p2@uc010ofi.1
Hg19::chr1:31886034..31886099,+p1@SERINC2
Hg19::chr1:35220613..35220718,+p1@GJB5
Hg19::chr1:35220725..35220754,+p2@GJB5
Hg19::chr1:35247024..35247046,+p4@GJB3
Hg19::chr1:35247057..35247079,+p3@GJB3
Hg19::chr1:35247081..35247102,+p6@GJB3
Hg19::chr1:44399399..44399444,+p1@ARTN
Hg19::chr1:44399451..44399461,+p6@ARTN
Hg19::chr1:44399466..44399482,+p3@ARTN
Hg19::chr1:44401579..44401643,+p2@ARTN
Hg19::chr1:6479968..6479986,-p1@HES2
Hg19::chr20:60953877..60953897,-p@chr20:60953877..60953897
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Hg19::chr22:38302285..38302361,+p1@MICALL1
Hg19::chr2:20424783..20424794,-p4@SDC1
Hg19::chr2:74669009..74669077,-p1@RTKN
Hg19::chr3:12800751..12800777,-p1@TMEM40
Hg19::chr6:30850697..30850739,+p2@DDR1
Hg19::chr6:35360450..35360509,+p@chr6:35360450..35360509
+
Hg19::chr7:150811705..150811763,+p4@AGAP3
Hg19::chr8:144815895..144815912,-p4@FAM83H
Hg19::chr8:144815914..144815961,-p1@FAM83H
Hg19::chr8:144815966..144815986,-p2@FAM83H
Hg19::chrX:54501038..54501075,-p@chrX:54501038..54501075
-


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
7.90940612888754e-050.0166888469319527385ECM-receptor interaction (KEGG):04512
6.12511642504549e-070.000387719869705379469Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
2.40906544721509e-060.000762469214043575497Cell junction organization (Reactome):REACT_20676
0.0001716388889811010.02716185418125924288{ACTB,297} (Static Module):NA



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:0009888tissue development0.000467859320844482
GO:0007398ectoderm development0.000467859320844482
GO:0014704intercalated disc0.000494265234320962
GO:0048731system development0.00501723215290283
GO:0007275multicellular organismal development0.00501723215290283
GO:0048513organ development0.00501723215290283
GO:0008544epidermis development0.0050388845571958
GO:0005922connexon complex0.00705063890640088
GO:0032502developmental process0.00733551717943004
GO:0005911intercellular junction0.00733551717943004
GO:0005921gap junction0.00749484253179777
GO:0048856anatomical structure development0.00749484253179777
GO:0022610biological adhesion0.00964929591541734
GO:0007155cell adhesion0.00964929591541734
GO:0032501multicellular organismal process0.0122266281545092
GO:0005604basement membrane0.0247177030320746
GO:0005610laminin-5 complex0.0273908549258614
GO:0008426protein kinase C inhibitor activity0.038791147396166
GO:0005515protein binding0.0448481256440162
GO:0043403skeletal muscle regeneration0.0465343065901034
GO:0030054cell junction0.0468426097393087
GO:0017049GTP-Rho binding0.0468426097393087
GO:0005916fascia adherens0.0468426097393087
GO:0005243gap junction channel activity0.0468426097393087
GO:0044459plasma membrane part0.0468426097393087
GO:0044420extracellular matrix part0.0468426097393087
GO:0022829wide pore channel activity0.0481077772224277
GO:0043588skin development0.0481077772224277
GO:0009898internal side of plasma membrane0.0481077772224277



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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell8.00e-61254
endodermal cell1.39e-1959
endo-epithelial cell1.01e-1843
embryonic cell3.24e-17248
squamous epithelial cell6.11e-1462
respiratory epithelial cell6.59e-0913
epithelial cell of alimentary canal2.29e-0821
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.37e-32169
endoderm2.37e-32169
presumptive endoderm2.37e-32169
digestive system1.34e-25155
digestive tract1.34e-25155
primitive gut1.34e-25155
subdivision of digestive tract1.18e-22129
endodermal part of digestive tract1.18e-22129
mixed endoderm/mesoderm-derived structure2.14e-22130
multi-tissue structure1.46e-21347
mesenchyme3.89e-20238
entire embryonic mesenchyme3.89e-20238
immaterial anatomical entity7.89e-19126
multi-cellular organism5.25e-18659
respiratory system1.37e-1772
anatomical space1.84e-17104
foregut2.37e-1798
trunk region element5.29e-17107
embryo2.00e-16612
anatomical system2.54e-16625
primordium2.55e-16168
anatomical group4.72e-16626
organism subdivision1.39e-15365
embryonic structure2.02e-14605
developing anatomical structure2.02e-14605
organ3.08e-14511
germ layer4.43e-14604
embryonic tissue4.43e-14604
presumptive structure4.43e-14604
epiblast (generic)4.43e-14604
trunk4.62e-14216
respiratory tract2.26e-1353
organ part2.32e-13219
endo-epithelium9.79e-1382
subdivision of trunk1.13e-12113
cell layer2.78e-12312
anatomical cluster3.48e-12286
epithelium3.80e-12309
renal system1.23e-1145
urinary system structure2.25e-1144
respiratory primordium2.83e-1138
endoderm of foregut2.83e-1138
anatomical conduit1.03e-10241
segment of respiratory tract1.59e-1046
organ segment4.14e-1097
epithelial bud8.46e-1037
orifice9.15e-1035
reproductive structure1.36e-0959
reproductive system1.36e-0959
anatomical cavity1.38e-0970
epithelial fold3.75e-0951
thoracic cavity element4.07e-0934
thoracic cavity4.07e-0934
thoracic segment organ7.89e-0935
intermediate mesoderm1.47e-0837
thoracic segment of trunk3.23e-0852
reproductive organ6.39e-0848
female organism1.06e-0741
body cavity precursor2.44e-0763
cavitated compound organ2.54e-0732
oral opening2.85e-0721
compound organ3.36e-0769
abdomen element4.48e-0755
abdominal segment element4.48e-0755
subdivision of head5.13e-0748
duct6.13e-0726
gland6.80e-0759
kidney7.16e-0727
kidney mesenchyme7.16e-0727
kidney rudiment7.16e-0727
kidney field7.16e-0727
Disease
Ontology termp-valuen
carcinoma2.17e-26106
cell type cancer1.61e-18143
squamous cell carcinoma1.33e-0814
adenocarcinoma2.36e-0825


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)

{{{tfbs_overrepresentation_jaspar}}}



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
CTCF#10664211.786752124358340.003956454479980330.0189928364329227
E2F1#1869231.791586538765470.002254273795155510.012804378141744
MYC#4609221.823653986911220.002340236975681950.0132673981925549
POLR2A#5430592.011106943125811.33117697459636e-152.46939239875433e-13
SMARCC1#659964.158415173298240.003206063014016610.0168167352278078
STAT3#6774152.504634523131960.0006787194324858910.00547457358737983
TFAP2A#7020102.622005456038880.004391873499157240.0208132714574137
TFAP2C#7022172.916775974089274.14543338165909e-050.00075229351337462
ZEB1#6935205.361406989696463.10677472077757e-103.12891461006065e-08



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

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