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Coexpression cluster:C2320

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Full id: C2320_neuroblastoma_cerebellum_retinoblastoma_pituitary_rectum_putamen_pineal



Phase1 CAGE Peaks

Hg19::chr14:89259135..89259181,-p2@EML5
Hg19::chr14:89259211..89259225,-p3@EML5
Hg19::chr14:89259247..89259263,-p6@EML5
Hg19::chr14:89259268..89259310,-p1@EML5


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
lymphocyte3.21e-0853
common lymphoid progenitor3.21e-0853
lymphoid lineage restricted progenitor cell3.47e-0852
Uber Anatomy
Ontology termp-valuen
adult organism7.59e-36115
neural tube5.57e-3157
neural rod5.57e-3157
future spinal cord5.57e-3157
neural keel5.57e-3157
central nervous system1.42e-2682
regional part of nervous system2.44e-2694
nervous system2.44e-2694
regional part of brain3.40e-2559
regional part of forebrain4.80e-2541
forebrain4.80e-2541
future forebrain4.80e-2541
brain1.55e-2469
future brain1.55e-2469
anterior neural tube6.96e-2442
neural plate4.81e-2286
presumptive neural plate4.81e-2286
neurectoderm1.00e-2090
gray matter1.02e-2034
brain grey matter1.02e-2034
telencephalon1.57e-2034
regional part of telencephalon6.75e-2033
cerebral hemisphere1.26e-1932
pre-chordal neural plate8.21e-1761
regional part of cerebral cortex5.94e-1622
cerebral cortex4.43e-1525
pallium4.43e-1525
anterior region of body4.84e-15129
craniocervical region4.84e-15129
neocortex1.33e-1420
head3.26e-14123
ectoderm-derived structure9.61e-12169
ectoderm2.78e-11173
presumptive ectoderm2.78e-11173
posterior neural tube3.25e-0815
chordal neural plate3.25e-0815
nucleus of brain3.96e-079
neural nucleus3.96e-079
basal ganglion4.66e-079
nuclear complex of neuraxis4.66e-079
aggregate regional part of brain4.66e-079
collection of basal ganglia4.66e-079
cerebral subcortex4.66e-079
segmental subdivision of nervous system4.96e-0713


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#90546.336201576962630.0006203100587215640.00511645571180078
CTCF#1066445.360256373075030.001211145381643620.00816333091406765
E2F1#186944.907389214879320.001724022357361790.0106377863039411
EGR1#195844.988179094810140.001615011500076050.0101346022986507
HMGN3#932448.178547723350590.0002234570284440470.00247877096055952
RAD21#5885410.35503389545638.6948481184721e-050.00129172296251082
REST#597837.237521537096020.004104697304192610.0195766956686716
TAF1#687243.343046285745290.008005664898701650.0321714431627035
ZBTB7A#5134147.35190930787590.000342223540015990.00346164496810944



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.