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Coexpression cluster:C4850: Difference between revisions

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|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157841294376558!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248201090902906!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546426774077141!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110309604028753
|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157841294376558!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248201090902906!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546426774077141!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110309604028753
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}}
}}

Revision as of 17:00, 26 November 2012


Full id: C4850_H9_HES3GFP_teratocarcinoma_testicular_Preadipocyte_anaplastic_iPS



Phase1 CAGE Peaks

Hg19::chrX:132549456..132549473,-p2@GPC4
Hg19::chrX:132549482..132549493,-p4@GPC4
Hg19::chrX:132549506..132549526,-p1@GPC4


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
fat cell8.59e-0715
Uber Anatomy
Ontology termp-valuen
adult organism2.32e-20114
multi-cellular organism2.53e-18656
central nervous system1.40e-1581
neural plate3.62e-1482
presumptive neural plate3.62e-1482
organ1.13e-13503
neural tube1.74e-1356
neural rod1.74e-1356
future spinal cord1.74e-1356
neural keel1.74e-1356
ectoderm-derived structure3.16e-13171
ectoderm3.16e-13171
presumptive ectoderm3.16e-13171
anatomical system7.04e-13624
neurectoderm7.05e-1386
anatomical group1.25e-12625
regional part of nervous system1.68e-1253
regional part of brain1.68e-1253
nervous system2.27e-1289
brain1.75e-1168
future brain1.75e-1168
ecto-epithelium3.89e-11104
structure with developmental contribution from neural crest3.98e-10132
embryo7.69e-10592
organ part1.33e-09218
regional part of forebrain2.48e-0941
forebrain2.48e-0941
anterior neural tube2.48e-0941
future forebrain2.48e-0941
pre-chordal neural plate3.23e-0961
organ system subdivision4.46e-09223
multi-tissue structure2.02e-08342
developing anatomical structure4.63e-08581
brain grey matter4.97e-0834
gray matter4.97e-0834
telencephalon8.63e-0834
regional part of telencephalon1.95e-0732
cerebral hemisphere2.62e-0732


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
JUND#372736.994663941871030.002921845042734990.0157841294376558
SP1#666735.69838137814090.005403962701712170.0248201090902906
TAF7#6879311.43306940492390.0006690181981945830.00546426774077141
ZNF263#1012738.221841637010680.001799043925565870.0110309604028753



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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