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Coexpression cluster:C3715

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Full id: C3715_occipital_paracentral_medial_amygdala_postcentral_parietal_brain



Phase1 CAGE Peaks

Hg19::chr18:29265234..29265252,-p@chr18:29265234..29265252
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Hg19::chr18:29265256..29265304,-p@chr18:29265256..29265304
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Hg19::chr18:29265316..29265333,-p@chr18:29265316..29265333
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube6.01e-2357
neural rod6.01e-2357
future spinal cord6.01e-2357
neural keel6.01e-2357
brain1.59e-2269
future brain1.59e-2269
neural plate1.88e-2286
presumptive neural plate1.88e-2286
central nervous system5.14e-2282
regional part of brain3.64e-2159
regional part of nervous system1.18e-2094
nervous system1.18e-2094
regional part of forebrain1.18e-1941
forebrain1.18e-1941
future forebrain1.18e-1941
anterior neural tube1.82e-1942
neurectoderm2.24e-1990
epithelium1.18e-17309
pre-chordal neural plate1.75e-1761
cell layer1.91e-17312
tube9.49e-17194
cerebral hemisphere1.29e-1632
gray matter2.42e-1634
brain grey matter2.42e-1634
telencephalon2.43e-1634
head3.60e-16123
regional part of telencephalon1.12e-1533
anterior region of body1.32e-15129
craniocervical region1.32e-15129
ectoderm-derived structure2.44e-15169
anatomical conduit3.79e-15241
anatomical cluster1.01e-14286
adult organism1.78e-14115
ectoderm1.11e-13173
presumptive ectoderm1.11e-13173
regional part of cerebral cortex1.74e-1322
cerebral cortex2.27e-1325
pallium2.27e-1325
neocortex2.63e-1220
organism subdivision7.38e-11365
multi-tissue structure5.62e-10347
organ part8.96e-10219


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#1066435.360256373075030.0064925092527670.0279271488405986
E2F1#186934.907389214879320.008460985347239390.0325112895025877
E2F6#187635.017155731697390.00791769806886330.0321957821450714
EBF1#187938.9064668465690.00141523283560980.00914694610546769
EGR1#195834.988179094810140.008056488137383440.0320464489861437
ELF1#199734.258097958807540.01295179875054610.0461962675355447
GABPB1#255337.067683836182170.002832212825417420.0154018992592434
NFKB1#479035.488063424193840.006049381815655430.0269455106173599
PAX5#507936.669565531177830.003370290999677260.0172823597837332
SRF#6722313.79717826216780.0003806615025800190.00374878893615791
TAF7#6879311.43306940492390.0006690181981945830.0054252342263564
YY1#752834.911170749853860.008441455341808260.0329145848214715



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.