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Coexpression cluster:C2705: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998104607808436!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392112557525885!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768647305722571!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797455753350028!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685081554273254!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.8348306957551e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322795010561154!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106986070417643!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304933842779453
|tf_chipseq_enrich=E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998104607808436!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392112557525885!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768647305722571!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797455753350028!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685081554273254!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.8348306957551e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322795010561154!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106986070417643!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304933842779453
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}}
}}

Revision as of 15:40, 26 November 2012


Full id: C2705_kidney_brain_occipital_duodenum_Neurons_Renal_temporal



Phase1 CAGE Peaks

Hg19::chr2:73144617..73144654,+p1@EMX1
Hg19::chr2:73144668..73144679,+p5@EMX1
Hg19::chr2:73144683..73144697,+p3@EMX1
Hg19::chr2:73144739..73144750,+p4@EMX1


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 cell7.53e-138
neural cell3.15e-1225
neuron2.82e-096
neuroblast2.82e-096
electrically signaling cell2.82e-096
astrocyte of the cerebral cortex4.22e-073
Uber Anatomy
Ontology termp-valuen
cerebral cortex3.79e-5025
pallium3.79e-5025
cerebral hemisphere1.02e-4432
telencephalon1.28e-4434
regional part of cerebral cortex1.46e-4422
regional part of telencephalon4.43e-4132
neocortex5.91e-4120
brain grey matter2.96e-3834
gray matter2.96e-3834
central nervous system1.37e-3681
regional part of forebrain1.09e-3541
forebrain1.09e-3541
anterior neural tube1.09e-3541
future forebrain1.09e-3541
nervous system9.11e-3289
brain2.12e-2668
future brain2.12e-2668
regional part of nervous system8.25e-2653
regional part of brain8.25e-2653
neural tube5.34e-2456
neural rod5.34e-2456
future spinal cord5.34e-2456
neural keel5.34e-2456
pre-chordal neural plate4.63e-2361
organ system subdivision1.84e-16223
neural plate4.52e-1582
presumptive neural plate4.52e-1582
neurectoderm5.31e-1486
gyrus9.09e-146
ectoderm-derived structure7.31e-13171
ectoderm7.31e-13171
presumptive ectoderm7.31e-13171
occipital lobe1.63e-125
ecto-epithelium3.64e-12104
parietal lobe3.96e-125
temporal lobe1.08e-116
limbic system5.27e-115
adult organism1.70e-09114
structure with developmental contribution from neural crest2.44e-09132
anatomical cluster3.19e-08373
frontal cortex1.07e-073


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
E2F6#187645.017155731697390.00157802193473060.00998104607808436
JUND#372746.994663941871030.000417684217818580.00392112557525885
NFKB1#479045.488063424193840.001102199566301980.00768647305722571
SIN3A#2594245.408884726815140.001168172384885160.00797455753350028
SP1#666745.69838137814090.0009482606065333980.00685081554273254
SUZ12#23512450.11578091106291.5827390373096e-078.8348306957551e-06
TAF1#687243.343046285745290.008005664898701650.0322795010561154
YY1#752844.911170749853860.00171871838055440.0106986070417643
ZEB1#6935416.88843201754391.22862303393937e-050.000304933842779453



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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