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Coexpression cluster:C1249: Difference between revisions

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|tf_chipseq_enrich=JUND#3727;7:6.99466394187103:1.21993360047445e-06:4.92686176720615e-05!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223491572591711!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211675392659364!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246712386023872!TBP#6908;7:3.70677068709639:0.000103967209750511:0.00145163521646172
|tf_chipseq_enrich=JUND#3727;7:6.99466394187103:1.21993360047445e-06:4.92686176720615e-05!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223491572591711!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211675392659364!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246712386023872!TBP#6908;7:3.70677068709639:0.000103967209750511:0.00145163521646172
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}}
}}

Revision as of 14:46, 26 November 2012


Full id: C1249_Melanocyte_anaplastic_Wilms_retina_heart_optic_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr1:150230160..150230176,+p4@CA14
Hg19::chr1:150230182..150230198,+p7@CA14
Hg19::chr1:150230212..150230227,+p5@CA14
Hg19::chr1:150230231..150230242,+p6@CA14
Hg19::chr1:150230247..150230279,+p2@CA14
Hg19::chr1:150230291..150230323,+p3@CA14
Hg19::chr1:150230431..150230501,+p1@CA14


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
pigment cell3.90e-1614
melanocyte4.74e-1410
melanoblast4.74e-1410
embryonic stem cell8.98e-105
visual pigment cell6.70e-074
Uber Anatomy
Ontology termp-valuen
adult organism1.39e-44114
neural tube6.45e-4156
neural rod6.45e-4156
future spinal cord6.45e-4156
neural keel6.45e-4156
regional part of nervous system4.07e-3753
regional part of brain4.07e-3753
central nervous system7.45e-3781
nervous system8.96e-3789
neural plate1.09e-3682
presumptive neural plate1.09e-3682
neurectoderm1.03e-3586
regional part of forebrain4.63e-2941
forebrain4.63e-2941
anterior neural tube4.63e-2941
future forebrain4.63e-2941
telencephalon5.56e-2934
brain7.45e-2968
future brain7.45e-2968
brain grey matter9.11e-2934
gray matter9.11e-2934
ecto-epithelium3.71e-28104
regional part of telencephalon3.23e-2632
cerebral hemisphere4.09e-2632
pre-chordal neural plate6.83e-2661
structure with developmental contribution from neural crest1.76e-24132
ectoderm-derived structure7.62e-22171
ectoderm7.62e-22171
presumptive ectoderm7.62e-22171
organ system subdivision4.45e-19223
cerebral cortex4.94e-1825
pallium4.94e-1825
regional part of cerebral cortex4.03e-1722
neocortex4.99e-1720
anatomical cluster3.83e-13373
neural nucleus8.10e-139
nucleus of brain8.10e-139
posterior neural tube9.03e-1315
chordal neural plate9.03e-1315
segmental subdivision of nervous system1.35e-1013
brainstem3.07e-106
telencephalic nucleus3.44e-107
basal ganglion1.00e-099
nuclear complex of neuraxis1.00e-099
aggregate regional part of brain1.00e-099
collection of basal ganglia1.00e-099
cerebral subcortex1.00e-099
tube1.79e-09192
multi-tissue structure3.44e-09342
segmental subdivision of hindbrain3.80e-0912
hindbrain3.80e-0912
presumptive hindbrain3.80e-0912
anatomical conduit3.24e-08240
occipital lobe6.99e-085
organ part2.82e-07218
retina4.66e-076
photoreceptor array4.66e-076
posterior segment of eyeball4.66e-076
layer of retina6.92e-074
epithelium8.12e-07306


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#372776.994663941871031.21993360047445e-064.92686176720615e-05
POLR2A#543072.147453176558070.004747636447610280.0223491572591711
SIN3A#2594275.408884726815147.3795239773719e-060.000211675392659364
TAF1#687273.343046285745290.0002142336319622450.00246712386023872
TBP#690873.706770687096390.0001039672097505110.00145163521646172



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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