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Coexpression cluster:C4835: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00130114615933376!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191430917689554!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663248301911973!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324803200681101!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465427832539064!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00584975653595772!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107787727537765!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187629945907639!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000723595064960936!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191396297722793!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423494840229661
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00130114615933376!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191430917689554!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663248301911973!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324803200681101!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465427832539064!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00584975653595772!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107787727537765!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187629945907639!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000723595064960936!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191396297722793!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423494840229661
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}}
}}

Revision as of 16:59, 26 November 2012


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
embryonic stem cell6.50e-095
Uber Anatomy
Ontology termp-valuen
neural tube1.87e-2056
neural rod1.87e-2056
future spinal cord1.87e-2056
neural keel1.87e-2056
regional part of nervous system1.42e-1853
regional part of brain1.42e-1853
adult organism1.54e-15114
nervous system1.59e-1589
brain8.63e-1568
future brain8.63e-1568
central nervous system1.70e-1481
brain grey matter6.10e-1434
gray matter6.10e-1434
neurectoderm9.90e-1486
telencephalon1.06e-1334
neural plate1.23e-1382
presumptive neural plate1.23e-1382
cerebral hemisphere2.77e-1332
regional part of cerebral cortex1.68e-1222
gastrointestinal system2.23e-1225
intestine2.45e-1217
neocortex4.37e-1220
regional part of forebrain7.82e-1241
forebrain7.82e-1241
anterior neural tube7.82e-1241
future forebrain7.82e-1241
regional part of telencephalon8.09e-1232
organ system subdivision1.63e-11223
posterior neural tube8.71e-1115
chordal neural plate8.71e-1115
cerebral cortex1.19e-1025
pallium1.19e-1025
brainstem2.64e-106
ecto-epithelium8.04e-10104
large intestine4.46e-0911
segmental subdivision of hindbrain8.11e-0912
hindbrain8.11e-0912
presumptive hindbrain8.11e-0912
segmental subdivision of nervous system5.06e-0813
lower digestive tract2.41e-075
pre-chordal neural plate2.42e-0761
small intestine6.23e-074
temporal lobe8.54e-076


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.

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