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Coexpression cluster:C3744

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Full id: C3744_salivary_adenocarcinoma_lung_ductal_amniotic_serous_chorionic



Phase1 CAGE Peaks

Hg19::chr18:9475001..9475037,+p2@RALBP1
Hg19::chr18:9475039..9475048,+p13@RALBP1
Hg19::chr18:9475057..9475066,+p9@RALBP1


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


No GOStat results

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 cell2.05e-27254
endo-epithelial cell2.34e-1443
embryonic cell8.55e-11248
endodermal cell1.82e-1059
squamous epithelial cell3.02e-0862
epithelial cell of alimentary canal4.42e-0821
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.24e-18169
endoderm2.24e-18169
presumptive endoderm2.24e-18169
digestive system5.62e-14155
digestive tract5.62e-14155
primitive gut5.62e-14155
mesenchyme9.23e-13238
entire embryonic mesenchyme9.23e-13238
multi-cellular organism1.58e-12659
mixed endoderm/mesoderm-derived structure6.40e-12130
subdivision of digestive tract1.33e-11129
endodermal part of digestive tract1.33e-11129
trunk5.01e-11216
organism subdivision6.37e-11365
surface structure2.30e-1095
anatomical system2.16e-09625
orifice2.91e-0935
organ component layer3.17e-0957
anatomical group3.78e-09626
respiratory system3.83e-0972
anatomical space5.41e-09104
multi-tissue structure1.20e-08347
extraembryonic membrane1.57e-0814
membranous layer1.57e-0814
organ1.95e-08511
reproductive structure4.11e-0859
reproductive system4.11e-0859
hindgut5.15e-0719
immaterial anatomical entity8.31e-07126
Disease
Ontology termp-valuen
carcinoma8.89e-11106
cell type cancer1.75e-08143


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#1066435.360256373075030.0064925092527670.0279363535699462
E2F1#186934.907389214879320.008460985347239390.0325232553802111
E2F6#187635.017155731697390.00791769806886330.0322070679109645
EBF1#187938.9064668465690.00141523283560980.00914807836344942
MYC#460935.22228187160940.007020843755740150.0294359655160877
NFKB1#479035.488063424193840.006049381815655430.0269535574848651
NR3C1#2908314.9730233311730.0002978331194675480.00308861018410002
NRF1#4899312.21027944771090.0005492172401020010.00471088200878884
RAD21#5885310.35503389545630.0009004912073565420.00663981934517861
SETDB1#9869340.32002617801051.52461559299059e-050.000358624612424199
SMARCC2#6601262.77024961793170.0003358375417085070.00341723860273721
SREBF1#6720231.33723296032550.00133816265136180.00887567440274199
STAT3#6774310.51946499715420.0008589184530415310.00642629015812053
TAF7#6879311.43306940492390.0006690181981945830.00542649826042591
TRIM28#10155318.59052504526250.0001555969297255280.00196998275471019



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.