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Coexpression cluster:C2127: Difference between revisions

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|tf_chipseq_enrich=RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129098840296433!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321232379113071!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248098890627694
|tf_chipseq_enrich=RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129098840296433!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321232379113071!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248098890627694
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}}
}}

Revision as of 15:18, 26 November 2012


Full id: C2127_parietal_acute_occipital_thyroid_glioblastoma_transitionalcell_putamen



Phase1 CAGE Peaks

Hg19::chr11:30607819..30607867,-p2@MPPED2
Hg19::chr11:30607871..30607882,-p6@MPPED2
Hg19::chr11:30607891..30607935,-p1@MPPED2
Hg19::chr11:30608144..30608178,-p4@MPPED2


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
neuronal stem cell3.34e-078
Uber Anatomy
Ontology termp-valuen
adult organism1.55e-54114
central nervous system2.15e-3781
neural tube4.71e-3656
neural rod4.71e-3656
future spinal cord4.71e-3656
neural keel4.71e-3656
regional part of nervous system3.81e-3453
regional part of brain3.81e-3453
nervous system9.99e-3489
regional part of forebrain3.35e-2941
forebrain3.35e-2941
anterior neural tube3.35e-2941
future forebrain3.35e-2941
brain2.98e-2868
future brain2.98e-2868
neural plate4.35e-2682
presumptive neural plate4.35e-2682
telencephalon9.43e-2634
brain grey matter9.59e-2634
gray matter9.59e-2634
cerebral hemisphere3.75e-2532
regional part of telencephalon1.48e-2432
neurectoderm1.92e-2486
ectoderm-derived structure4.55e-21171
ectoderm4.55e-21171
presumptive ectoderm4.55e-21171
ecto-epithelium3.08e-20104
pre-chordal neural plate3.69e-1961
cerebral cortex4.10e-1925
pallium4.10e-1925
organ system subdivision5.00e-19223
regional part of cerebral cortex2.14e-1722
structure with developmental contribution from neural crest8.21e-17132
neocortex5.12e-1620
anatomical cluster2.33e-08373
posterior neural tube4.12e-0815
chordal neural plate4.12e-0815
basal ganglion4.17e-089
nuclear complex of neuraxis4.17e-089
aggregate regional part of brain4.17e-089
collection of basal ganglia4.17e-089
cerebral subcortex4.17e-089
neural nucleus4.59e-089
nucleus of brain4.59e-089
segmental subdivision of nervous system3.90e-0713
telencephalic nucleus6.21e-077


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
RAD21#5885410.35503389545638.6948481184721e-050.00129098840296433
TAF1#687243.343046285745290.008005664898701650.0321232379113071
ZNF263#1012748.221841637010680.0002187871180958320.00248098890627694



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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