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Coexpression cluster:C3292: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3292_optic_Mesenchymal_aorta_heart_gall_globus_penis
|full_id=C3292_optic_Mesenchymal_aorta_heart_gall_globus_penis
|id=C3292
|id=C3292

Revision as of 16:11, 12 September 2012


Full id: C3292_optic_Mesenchymal_aorta_heart_gall_globus_penis



Phase1 CAGE Peaks

Hg19::chr12:53440813..53440830,-p1@ENST00000546566
Hg19::chr12:53440842..53440861,-p1@uc001sbj.1
Hg19::chr12:53440983..53441061,+p@chr12:53440983..53441061
+


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
non-terminally differentiated cell4.26e-09180
fibroblast8.30e-0875
fat cell8.09e-0715
Uber Anatomy
Ontology termp-valuen
adult organism5.58e-41115
organism subdivision5.98e-28365
neural tube2.31e-2557
neural rod2.31e-2557
future spinal cord2.31e-2557
neural keel2.31e-2557
regional part of brain1.78e-2359
neural plate9.42e-2286
presumptive neural plate9.42e-2286
brain1.00e-2169
future brain1.00e-2169
multi-tissue structure1.92e-21347
neurectoderm1.20e-2090
central nervous system2.25e-2082
anatomical cluster3.31e-19286
anterior neural tube6.06e-1942
head1.87e-18123
regional part of forebrain2.18e-1841
forebrain2.18e-1841
future forebrain2.18e-1841
anterior region of body4.27e-18129
craniocervical region4.27e-18129
ectoderm-derived structure1.81e-17169
regional part of nervous system2.30e-1794
nervous system2.30e-1794
anatomical conduit3.93e-17241
ectoderm5.61e-17173
presumptive ectoderm5.61e-17173
gray matter2.20e-1534
brain grey matter2.20e-1534
telencephalon3.02e-1534
tube3.12e-15194
cell layer5.92e-15312
multi-cellular organism6.19e-15659
regional part of telencephalon8.57e-1533
epithelium9.77e-15309
organ1.90e-14511
pre-chordal neural plate2.48e-1461
cerebral hemisphere5.70e-1432
organ part5.08e-12219
anatomical system1.41e-11625
anatomical group2.71e-11626
regional part of cerebral cortex6.38e-1122
cerebral cortex3.14e-1025
pallium3.14e-1025
neocortex6.82e-1020
embryonic structure2.21e-08605
developing anatomical structure2.21e-08605
germ layer3.14e-08604
embryonic tissue3.14e-08604
presumptive structure3.14e-08604
epiblast (generic)3.14e-08604
embryo4.02e-08612
posterior neural tube1.34e-0715
chordal neural plate1.34e-0715
nucleus of brain6.90e-079
neural nucleus6.90e-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
CCNT2#90536.336201576962630.003930750035764890.0189452029620771
CTCF#1066435.360256373075030.0064925092527670.0278674656357773
E2F1#186934.907389214879320.008460985347239390.0324099339328933
EGR1#195834.988179094810140.008056488137383440.0319466764591157
ELF1#199734.258097958807540.01295179875054610.0460625522614004
GABPB1#255337.067683836182170.002832212825417420.0153730822344873
SPI1#668838.204323508522730.001810593189410520.010890148704725
ZNF263#1012738.221841637010680.001799043925565870.0109042045465831



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.