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Coexpression cluster:C3182: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323802436306462!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320622104072744
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323802436306462!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320622104072744
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}}
}}

Revision as of 15:58, 26 November 2012


Full id: C3182_skeletal_diaphragm_Pericytes_tongue_optic_corpus_Skeletal



Phase1 CAGE Peaks

Hg19::chr11:63933372..63933383,-p7@MACROD1
Hg19::chr2:127864608..127864688,-p1@BIN1
Hg19::chr2:127864693..127864713,-p4@BIN1


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
mesodermal cell1.17e-08121
contractile cell5.31e-0859
muscle precursor cell5.29e-0758
myoblast5.29e-0758
multi-potent skeletal muscle stem cell5.29e-0758
kidney cell8.37e-0717
kidney epithelial cell8.37e-0717
Uber Anatomy
Ontology termp-valuen
anatomical cluster7.01e-34373
multi-tissue structure9.29e-34342
cell layer8.56e-29309
epithelium7.30e-28306
brain1.90e-2568
future brain1.90e-2568
multi-cellular organism1.10e-23656
neural tube4.42e-2356
neural rod4.42e-2356
future spinal cord4.42e-2356
neural keel4.42e-2356
neural plate2.00e-2282
presumptive neural plate2.00e-2282
central nervous system2.89e-2281
anatomical conduit5.46e-22240
anatomical system6.74e-22624
embryo6.90e-22592
tube7.26e-22192
nervous system1.58e-2189
anatomical group1.65e-21625
regional part of nervous system2.25e-2153
regional part of brain2.25e-2153
developing anatomical structure1.97e-20581
organ system subdivision2.17e-20223
structure with developmental contribution from neural crest1.37e-19132
neurectoderm1.61e-1986
pre-chordal neural plate1.49e-1861
adult organism3.36e-18114
germ layer5.10e-18560
germ layer / neural crest5.10e-18560
embryonic tissue5.10e-18560
presumptive structure5.10e-18560
germ layer / neural crest derived structure5.10e-18560
epiblast (generic)5.10e-18560
embryonic structure8.58e-18564
regional part of forebrain1.09e-1741
forebrain1.09e-1741
anterior neural tube1.09e-1741
future forebrain1.09e-1741
organ4.03e-16503
mesenchyme6.18e-15160
entire embryonic mesenchyme6.18e-15160
brain grey matter7.32e-1534
gray matter7.32e-1534
telencephalon7.51e-1534
ecto-epithelium1.03e-14104
organ part9.53e-14218
regional part of telencephalon1.18e-1332
cerebral hemisphere1.40e-1332
ectoderm-derived structure4.54e-12171
ectoderm4.54e-12171
presumptive ectoderm4.54e-12171
regional part of cerebral cortex2.26e-1122
trunk mesenchyme1.84e-10122
neocortex2.81e-1020
epithelial vesicle4.93e-1078
cerebral cortex8.52e-1025
pallium8.52e-1025
organism subdivision5.17e-09264
muscle tissue7.13e-0964
musculature7.13e-0964
musculature of body7.13e-0964
skeletal muscle tissue8.34e-0962
striated muscle tissue8.34e-0962
myotome8.34e-0962
dense mesenchyme tissue1.55e-0873
paraxial mesoderm1.95e-0872
presumptive paraxial mesoderm1.95e-0872
unilaminar epithelium2.75e-08148
somite4.84e-0871
presomitic mesoderm4.84e-0871
presumptive segmental plate4.84e-0871
dermomyotome4.84e-0871
trunk paraxial mesoderm4.84e-0871
tissue6.23e-08773
epithelial tube8.96e-08117
trunk4.74e-07199
excretory tube4.78e-0716
kidney epithelium4.78e-0716
neural nucleus7.90e-079
nucleus of brain7.90e-079


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
E2F1#186934.907389214879320.008460985347239390.0323802436306462
E2F6#187635.017155731697390.00791769806886330.0320622104072744



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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