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Coexpression cluster:C4531: Difference between revisions

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|tf_chipseq_enrich=HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393071241446725!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246879379540212!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179797152285977!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157491006615504!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722699403834925!TAL1#6886;2:19.9124111182935:0.00328717660874055:0.017020795133379!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329406562842765!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109973865111018!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.38724791624585e-06
|tf_chipseq_enrich=HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393071241446725!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246879379540212!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179797152285977!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157491006615504!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722699403834925!TAL1#6886;2:19.9124111182935:0.00328717660874055:0.017020795133379!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329406562842765!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109973865111018!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.38724791624585e-06
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}}
}}

Revision as of 16:48, 26 November 2012


Full id: C4531_temporal_duodenum_Mesenchymal_occipital_parietal_Neurons_glioblastoma



Phase1 CAGE Peaks

Hg19::chr5:92919068..92919082,+p5@NR2F1
Hg19::chr5:92919100..92919135,+p3@NR2F1
Hg19::chr5:92919375..92919438,+p6@NR2F1


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><br>


Uber Anatomy
Ontology termp-valuen
anatomical cluster1.31e-29373
neural plate1.95e-2682
presumptive neural plate1.95e-2682
neurectoderm6.54e-2686
central nervous system4.31e-2581
neural tube1.39e-2456
neural rod1.39e-2456
future spinal cord1.39e-2456
neural keel1.39e-2456
multi-tissue structure1.75e-23342
regional part of nervous system1.37e-2253
regional part of brain1.37e-2253
brain2.63e-2268
future brain2.63e-2268
nervous system3.03e-2289
structure with developmental contribution from neural crest6.96e-22132
cell layer1.45e-21309
organ system subdivision5.78e-21223
anatomical conduit6.71e-21240
epithelium1.64e-20306
adult organism6.52e-19114
pre-chordal neural plate1.48e-1861
tube2.98e-18192
ecto-epithelium3.56e-18104
regional part of forebrain1.38e-1641
forebrain1.38e-1641
anterior neural tube1.38e-1641
future forebrain1.38e-1641
ectoderm-derived structure9.45e-16171
ectoderm9.45e-16171
presumptive ectoderm9.45e-16171
multi-cellular organism1.87e-15656
brain grey matter2.37e-1534
gray matter2.37e-1534
telencephalon2.81e-1534
cerebral hemisphere1.67e-1432
regional part of telencephalon2.01e-1432
cerebral cortex1.45e-1225
pallium1.45e-1225
organ part2.27e-12218
regional part of cerebral cortex1.32e-1122
anatomical system1.81e-11624
anatomical group2.90e-11625
embryo3.07e-11592
germ layer4.46e-11560
germ layer / neural crest4.46e-11560
embryonic tissue4.46e-11560
presumptive structure4.46e-11560
germ layer / neural crest derived structure4.46e-11560
epiblast (generic)4.46e-11560
embryonic structure8.44e-11564
neocortex9.07e-1120
developing anatomical structure1.15e-10581
organ4.16e-10503
posterior neural tube2.37e-0915
chordal neural plate2.37e-0915
organism subdivision3.04e-08264
organ segment5.05e-0898
segmental subdivision of nervous system1.93e-0713
mesenchyme2.13e-07160
entire embryonic mesenchyme2.13e-07160
segmental subdivision of hindbrain2.18e-0712
hindbrain2.18e-0712
presumptive hindbrain2.18e-0712


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
HDAC2#3066313.41562023662630.0004140761399857210.00393071241446725
HNF4A#3172215.42152690863580.005444210486686610.0246879379540212
HNF4G#3174219.16894835096450.003543986611284220.0179797152285977
JUND#372736.994663941871030.002921845042734990.0157491006615504
MXI1#460139.96157162875930.001011470541259020.00722699403834925
TAL1#6886219.91241111829350.003287176608740550.017020795133379
TRIM28#10155212.39368336350830.008368344129438470.0329406562842765
ZNF263#1012738.221841637010680.001799043925565870.0109973865111018
ZZZ3#260093239.4132124352337.25894005043406e-084.38724791624585e-06



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.