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Coexpression cluster:C511

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Full id: C511_Placental_Alveolar_Bronchial_amniotic_Gingival_Corneal_Mammary



Phase1 CAGE Peaks

Hg19::chr11:394157..394180,+p3@PKP3
Hg19::chr11:394196..394258,+p1@PKP3
Hg19::chr11:394263..394275,+p5@PKP3
Hg19::chr11:66824276..66824298,+p2@RHOD
Hg19::chr11:66824303..66824343,+p1@RHOD
Hg19::chr11:66824346..66824359,+p3@RHOD
Hg19::chr14:105330834..105330858,+p@chr14:105330834..105330858
+
Hg19::chr17:7284402..7284414,+p1@TNK1
Hg19::chr19:45843994..45844015,+p1@KLC3
Hg19::chr1:35246775..35246797,+p2@GJB3
Hg19::chr1:35246802..35246823,+p1@GJB3
Hg19::chr1:35247135..35247151,+p9@GJB3
Hg19::chr1:35247162..35247173,+p7@GJB3
Hg19::chr1:35247859..35247901,+p5@GJB3
Hg19::chr5:175843524..175843547,-p1@CLTB
Hg19::chr6:41604725..41604741,+p4@MDFI
Hg19::chr6:41604747..41604796,+p1@MDFI
Hg19::chr9:140506925..140506963,+p3@ARRDC1


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

No results for this coexpression

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:0014704intercalated disc0.00971357311575209
GO:0005911intercellular junction0.0328503730566494
GO:0009950dorsal/ventral axis specification0.0328503730566494
GO:0005243gap junction channel activity0.0328503730566494
GO:0022829wide pore channel activity0.0328503730566494
GO:0043392negative regulation of DNA binding0.0328503730566494
GO:0051100negative regulation of binding0.0328503730566494
GO:0042994cytoplasmic sequestering of transcription factor0.0328503730566494
GO:0030057desmosome0.0328503730566494
GO:0051220cytoplasmic sequestering of protein0.0328503730566494
GO:0042308negative regulation of protein import into nucleus0.0328503730566494
GO:0042992negative regulation of transcription factor import into nucleus0.0328503730566494
GO:0051101regulation of DNA binding0.0328503730566494
GO:0046823negative regulation of nucleocytoplasmic transport0.0328503730566494
GO:0051224negative regulation of protein transport0.0328503730566494
GO:0030132clathrin coat of coated pit0.0328503730566494
GO:0001890placenta development0.0328503730566494
GO:0030054cell junction0.0328503730566494
GO:0030130clathrin coat of trans-Golgi network vesicle0.0328503730566494
GO:0012510trans-Golgi network transport vesicle membrane0.0328503730566494
GO:0009798axis specification0.0328503730566494
GO:0030178negative regulation of Wnt receptor signaling pathway0.0328503730566494
GO:0005886plasma membrane0.0328503730566494
GO:0007257activation of JNK activity0.0328503730566494
GO:0042990regulation of transcription factor import into nucleus0.0328503730566494
GO:0042991transcription factor import into nucleus0.0328503730566494
GO:0030125clathrin vesicle coat0.0328503730566494
GO:0042306regulation of protein import into nucleus0.0328503730566494
GO:0033157regulation of intracellular protein transport0.0328503730566494
GO:0043507positive regulation of JNK activity0.0328503730566494
GO:0030665clathrin coated vesicle membrane0.0328503730566494
GO:0006886intracellular protein transport0.0328503730566494
GO:0032507maintenance of cellular protein localization0.0328503730566494
GO:0043506regulation of JNK activity0.0328503730566494
GO:0051651maintenance of cellular localization0.0328503730566494
GO:0032386regulation of intracellular transport0.0328503730566494
GO:0045185maintenance of protein localization0.0328503730566494
GO:0030111regulation of Wnt receptor signaling pathway0.0328503730566494
GO:0051223regulation of protein transport0.0328503730566494
GO:0009953dorsal/ventral pattern formation0.0328503730566494
GO:0005922connexon complex0.0328503730566494
GO:0051098regulation of binding0.0328503730566494
GO:0005871kinesin complex0.0328503730566494
GO:0046822regulation of nucleocytoplasmic transport0.0328503730566494
GO:0030140trans-Golgi network transport vesicle0.0328503730566494
GO:0051051negative regulation of transport0.0336156853620909
GO:0030658transport vesicle membrane0.0336156853620909
GO:0030660Golgi-associated vesicle membrane0.0339741446877352
GO:0005921gap junction0.0353546012067987
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0407401896373074
GO:0051235maintenance of localization0.040936282410428
GO:0044459plasma membrane part0.0413010282697245
GO:0005905coated pit0.0413057609230136
GO:0046777protein amino acid autophosphorylation0.0414799877126929
GO:0016540protein autoprocessing0.0425694626794528
GO:0030120vesicle coat0.0454288408777507
GO:0030662coated vesicle membrane0.0455204621896562
GO:0000187activation of MAPK activity0.049972168624338



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 cell3.50e-50254
endo-epithelial cell1.43e-1743
endodermal cell5.51e-1659
embryonic cell3.54e-15248
squamous epithelial cell2.50e-1162
epithelial cell of alimentary canal3.42e-0921
respiratory epithelial cell1.73e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.30e-26169
endoderm1.30e-26169
presumptive endoderm1.30e-26169
digestive system1.62e-20155
digestive tract1.62e-20155
primitive gut1.62e-20155
mesenchyme6.04e-18238
entire embryonic mesenchyme6.04e-18238
multi-tissue structure9.16e-18347
mixed endoderm/mesoderm-derived structure3.55e-17130
multi-cellular organism5.11e-17659
subdivision of digestive tract2.81e-16129
endodermal part of digestive tract2.81e-16129
immaterial anatomical entity2.75e-15126
respiratory system3.25e-1572
anatomical space1.71e-14104
trunk1.61e-13216
primordium2.94e-13168
organ part3.94e-12219
anatomical system5.07e-12625
foregut8.25e-1298
anatomical group8.89e-12626
organism subdivision1.22e-11365
subdivision of trunk1.47e-11113
embryo1.62e-11612
respiratory tract1.00e-1053
embryonic structure1.83e-10605
developing anatomical structure1.83e-10605
germ layer3.25e-10604
embryonic tissue3.25e-10604
presumptive structure3.25e-10604
epiblast (generic)3.25e-10604
orifice6.81e-1035
organ1.14e-09511
organ segment1.67e-0997
endo-epithelium1.85e-0982
anatomical cluster2.16e-09286
thoracic segment of trunk3.52e-0952
intermediate mesoderm3.86e-0937
respiratory primordium6.29e-0938
endoderm of foregut6.29e-0938
trunk region element7.03e-09107
epithelium7.34e-09309
segment of respiratory tract9.99e-0946
anatomical cavity1.12e-0870
cell layer1.17e-08312
reproductive structure1.61e-0859
reproductive system1.61e-0859
trunk mesenchyme3.81e-08143
epithelial fold4.80e-0851
oral opening1.05e-0721
extraembryonic membrane1.13e-0714
membranous layer1.13e-0714
subdivision of head1.14e-0748
anatomical conduit1.97e-07241
renal system2.76e-0745
urinary system structure3.64e-0744
epithelial bud4.82e-0737
female organism5.12e-0741
mesoderm5.49e-07448
mesoderm-derived structure5.49e-07448
presumptive mesoderm5.49e-07448
thoracic cavity element6.11e-0734
thoracic cavity6.11e-0734
mouth6.65e-0728
stomodeum6.65e-0728
reproductive organ7.03e-0748
Disease
Ontology termp-valuen
carcinoma5.51e-19106
cell type cancer1.60e-12143
adenocarcinoma6.25e-0925
squamous cell carcinoma2.45e-0814


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
E2F1#186992.453694607439660.004849080951923650.0227252934950843
GABPB1#255383.141192816080970.001854476277993430.0109435895579928
NR3C1#290864.991007777057680.0008156830055758030.0062150082016
POLR2A#5430182.147453176558071.059158074972e-064.41410256153236e-05
SMARCC1#659937.277226553271910.007571580574644320.0312075576634942



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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