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Coexpression cluster:C4835

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Full id: C4835_rhabdomyosarcoma_rectum_colon_stomach_duodenum_small_testis



Phase1 CAGE Peaks

Hg19::chr9:98279050..98279078,-p4@PTCH1
Hg19::chr9:98279086..98279094,-p15@PTCH1
Hg19::chr9:98279099..98279113,-p11@PTCH1


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism8.86e-27115
neural tube3.70e-2457
neural rod3.70e-2457
future spinal cord3.70e-2457
neural keel3.70e-2457
central nervous system2.38e-2382
regional part of nervous system1.84e-2294
nervous system1.84e-2294
neurectoderm4.04e-1990
regional part of brain1.26e-1859
brain5.51e-1869
future brain5.51e-1869
neural plate1.28e-1786
presumptive neural plate1.28e-1786
regional part of forebrain1.20e-1641
forebrain1.20e-1641
future forebrain1.20e-1641
gray matter4.28e-1634
brain grey matter4.28e-1634
anterior neural tube4.89e-1642
telencephalon7.27e-1634
regional part of telencephalon3.64e-1533
cerebral hemisphere1.50e-1432
regional part of cerebral cortex2.12e-1422
neocortex2.32e-1420
cerebral cortex4.79e-1225
pallium4.79e-1225
ectoderm2.50e-11173
presumptive ectoderm2.50e-11173
ectoderm-derived structure2.87e-10169
pre-chordal neural plate4.25e-1061
posterior neural tube1.47e-0915
chordal neural plate1.47e-0915
temporal lobe2.08e-097
head3.92e-08123
male reproductive organ5.67e-0811
anterior region of body9.90e-08129
craniocervical region9.90e-08129
testis3.60e-078
segmental subdivision of hindbrain8.23e-0712
hindbrain8.23e-0712
presumptive hindbrain8.23e-0712
Disease
Ontology termp-valuen
germ cell and embryonal cancer2.06e-0722
germ cell cancer2.06e-0722


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
ATF3#467322.46317452600878.81932387510763e-050.00130114615933376
CCNT2#90536.336201576962630.003930750035764890.0191430917689554
CHD2#1106310.34402283411690.0009033701102746880.00663248301911973
E2F6#187635.017155731697390.00791769806886330.0324803200681101
ELF1#199734.258097958807540.01295179875054610.0465427832539064
FOXA1#3169311.08141974938550.000734755275698670.00584975653595772
FOXA2#3170324.63046375266526.68983856509345e-050.00107787727537765
MAX#414936.452555509007120.003721913834265510.0187629945907639
TAL1#6886329.86861667744023.75103522793067e-050.000723595064960936
USF1#739136.361499277207960.00388404057290560.0191396297722793
USF2#7392312.99219738506960.0004558979393427810.00423494840229661



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.