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Coexpression cluster:C2125

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Full id: C2125_gastric_signet_Lens_Ciliary_lung_Hepatocyte_kidney



Phase1 CAGE Peaks

Hg19::chr11:27494245..27494278,-p5@LGR4
Hg19::chr11:27494279..27494308,-p3@LGR4
Hg19::chr11:27494309..27494328,-p2@LGR4
Hg19::chr11:27494329..27494347,-p1@LGR4


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 cell7.62e-07253
Uber Anatomy
Ontology termp-valuen
organ1.06e-16503
multi-cellular organism2.14e-15656
multi-tissue structure7.70e-15342
anatomical cluster1.55e-14373
primordium4.59e-12160
anatomical system9.48e-12624
anatomical group1.47e-11625
embryo1.96e-09592
organ system subdivision1.26e-08223
adult organism8.37e-08114
compound organ1.21e-0768
developing anatomical structure1.21e-07581
organ part2.35e-07218
reproductive organ2.55e-0748
epithelium2.73e-07306
cell layer3.30e-07309
digestive system3.59e-07145
digestive tract3.59e-07145
primitive gut3.59e-07145
ectoderm-derived structure3.80e-07171
ectoderm3.80e-07171
presumptive ectoderm3.80e-07171
external genitalia4.98e-0722
endoderm-derived structure5.23e-07160
endoderm5.23e-07160
presumptive endoderm5.23e-07160
gonad5.69e-0721
indifferent external genitalia5.69e-0721
indifferent gonad5.69e-0721
gonad primordium5.69e-0721
structure with developmental contribution from neural crest9.39e-07132
Disease
Ontology termp-valuen
cell type cancer4.82e-10143
carcinoma1.09e-08106


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
CEBPB#105147.971147625824820.0002476385788090830.00267595711663133
HEY1#2346244.040111043105710.00375304636917980.0185518936837736
IRF3#3661446.98195221148962.04940266214005e-071.10101627896731e-05
MXI1#460149.96157162875930.0001015224754950450.00142111055062686
NFYB#4801416.75979325353651.26678572070404e-050.000311005721402467
PBX3#5090421.91451268674414.33289161192893e-060.000135974419188175
POU2F2#545249.106124057742520.000145395665174930.00188025976661769
RFX5#5993412.04791082719514.74457429336527e-050.00082531411496465
SIN3A#2594245.408884726815140.001168172384885160.00794133669888829
SMARCB1#6598418.25271578115749.00423392720929e-060.00024075606429181
TAF1#687243.343046285745290.008005664898701650.0321220037786892
TAF7#6879411.43306940492395.85061525419808e-050.000967282581182829
TBP#690843.706770687096390.005296377814784350.0243473921650716



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.