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Coexpression cluster:C4440: Difference between revisions

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|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296402757627518!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.0088784396120378!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.017458743179875!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324884466318518!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381487362392106!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.026855272375187!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203264058050619!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287622767712597!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00561037879046403!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390315523185583!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329369320721471
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296402757627518!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.0088784396120378!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.017458743179875!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324884466318518!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381487362392106!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.026855272375187!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203264058050619!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287622767712597!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00561037879046403!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390315523185583!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329369320721471
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}}
}}

Revision as of 16:44, 26 November 2012


Full id: C4440_left_heart_medial_middle_parietal_hippocampus_occipital



Phase1 CAGE Peaks

Hg19::chr4:89205685..89205696,-p5@PPM1K
Hg19::chr4:89205705..89205720,-p1@PPM1K
Hg19::chr8:22861538..22861557,+p14@RHOBTB2


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
lymphocyte of B lineage1.95e-0924
pro-B cell1.95e-0924
nucleate cell8.41e-0755
lymphocyte9.59e-0753
common lymphoid progenitor9.59e-0753
Uber Anatomy
Ontology termp-valuen
adult organism3.38e-34114
neural tube1.29e-2556
neural rod1.29e-2556
future spinal cord1.29e-2556
neural keel1.29e-2556
regional part of nervous system7.15e-2453
regional part of brain7.15e-2453
regional part of forebrain3.77e-2141
forebrain3.77e-2141
anterior neural tube3.77e-2141
future forebrain3.77e-2141
central nervous system3.40e-2081
brain9.42e-1968
future brain9.42e-1968
nervous system5.56e-1889
telencephalon8.41e-1834
brain grey matter8.92e-1834
gray matter8.92e-1834
neural plate6.64e-1782
presumptive neural plate6.64e-1782
regional part of telencephalon1.30e-1632
cerebral hemisphere1.36e-1632
neurectoderm8.28e-1586
structure with developmental contribution from neural crest2.28e-14132
regional part of cerebral cortex2.34e-1322
cerebral cortex7.00e-1325
pallium7.00e-1325
neocortex2.68e-1220
ecto-epithelium4.17e-12104
pre-chordal neural plate5.57e-1261
ectoderm-derived structure1.13e-09171
ectoderm1.13e-09171
presumptive ectoderm1.13e-09171
organ system subdivision1.44e-08223


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
BRCA1#672213.45615376214920.007119807716084560.0296402757627518
IRF3#3661231.32130147432640.001339514673320110.0088784396120378
NANOG#79923219.49651898734180.003427255648501020.017458743179875
NFYA#4800212.28372046655370.008516011403724430.0324884466318518
NFYB#4801211.17319550235760.01025467135054530.0381487362392106
PBX3#5090214.60967512449610.006056122473217890.026855272375187
SP2#6668217.43568699589640.004273568481769740.0203264058050619
STAT1#6772213.80439166479950.006770931708444080.0287622767712597
STAT2#6773243.50918079096040.0006968990898868230.00561037879046403
TFAP2A#7020211.01242291536330.01054990655215560.0390315523185583
TRIM28#10155212.39368336350830.008368344129438470.0329369320721471



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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