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Coexpression cluster:C1856: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239376882294038!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121206969113912!TAF7#6879;3:6.85984164295435:0.00584328640701904:0.0262491715369548
|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239376882294038!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121206969113912!TAF7#6879;3:6.85984164295435:0.00584328640701904:0.0262491715369548
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}}
}}

Revision as of 15:09, 26 November 2012


Full id: C1856_brain_parietal_temporal_occipital_duodenum_Fibroblast_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr1:34286163..34286166,-p@chr1:34286163..34286166
-
Hg19::chr1:34630742..34630755,-p3@CSMD2
Hg19::chr1:34630758..34630772,-p2@CSMD2
Hg19::chr1:34630820..34630844,-p1@CSMD2
Hg19::chr1:34630978..34630987,-p5@CSMD2


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
skin fibroblast8.99e-1023
fibroblast7.75e-0776
Uber Anatomy
Ontology termp-valuen
central nervous system3.31e-3581
neural tube4.87e-3556
neural rod4.87e-3556
future spinal cord4.87e-3556
neural keel4.87e-3556
nervous system6.81e-3489
regional part of nervous system1.29e-3253
regional part of brain1.29e-3253
neurectoderm4.07e-2986
brain3.51e-2868
future brain3.51e-2868
neural plate5.94e-2882
presumptive neural plate5.94e-2882
brain grey matter7.86e-2734
gray matter7.86e-2734
regional part of forebrain1.36e-2641
forebrain1.36e-2641
anterior neural tube1.36e-2641
future forebrain1.36e-2641
telencephalon2.45e-2634
cerebral hemisphere3.58e-2532
regional part of telencephalon6.03e-2532
structure with developmental contribution from neural crest1.08e-21132
ecto-epithelium3.90e-21104
pre-chordal neural plate4.77e-2161
ectoderm-derived structure3.31e-20171
ectoderm3.31e-20171
presumptive ectoderm3.31e-20171
cerebral cortex7.65e-2025
pallium7.65e-2025
neocortex2.50e-1820
regional part of cerebral cortex6.30e-1822
adult organism1.11e-14114
tube2.40e-12192
organ system subdivision1.54e-09223
posterior neural tube1.75e-0915
chordal neural plate1.75e-0915
multi-cellular organism5.95e-09656
anatomical conduit1.53e-08240
neural nucleus2.04e-089
nucleus of brain2.04e-089
integument3.66e-0846
integumental system3.66e-0846
segmental subdivision of nervous system4.73e-0813
basal ganglion5.59e-089
nuclear complex of neuraxis5.59e-089
aggregate regional part of brain5.59e-089
collection of basal ganglia5.59e-089
cerebral subcortex5.59e-089
organ part7.15e-08218
skin of body7.84e-0841
segmental subdivision of hindbrain3.01e-0712
hindbrain3.01e-0712
presumptive hindbrain3.01e-0712
gyrus7.68e-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
CTCF#1066444.288205098460020.005152015588243280.0239376882294038
EP300#203345.419153380978560.00209386927943890.0121206969113912
TAF7#687936.859841642954350.005843286407019040.0262491715369548



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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