Personal tools

Coexpression cluster:C4153

From FANTOM5_SSTAR

Revision as of 16:34, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4153_cerebellum_Burkitt_eye_occipital_colon_caudate_retina



Phase1 CAGE Peaks

Hg19::chr2:180726040..180726052,-p2@ZNF385B
Hg19::chr2:180726058..180726098,-p3@ZNF385B
Hg19::chr2:180726254..180726275,-p4@ZNF385B


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
adult organism9.39e-65114
regional part of nervous system5.35e-4453
regional part of brain5.35e-4453
neural tube1.10e-4256
neural rod1.10e-4256
future spinal cord1.10e-4256
neural keel1.10e-4256
brain7.83e-4268
future brain7.83e-4268
central nervous system9.91e-4281
nervous system2.95e-3889
regional part of forebrain1.43e-3641
forebrain1.43e-3641
anterior neural tube1.43e-3641
future forebrain1.43e-3641
organ system subdivision2.38e-32223
cerebral hemisphere1.12e-3132
telencephalon2.42e-3134
brain grey matter4.59e-3134
gray matter4.59e-3134
neural plate1.66e-2982
presumptive neural plate1.66e-2982
regional part of telencephalon4.02e-2932
regional part of cerebral cortex1.71e-2722
neurectoderm2.41e-2786
neocortex1.94e-2520
pre-chordal neural plate1.15e-2461
cerebral cortex2.28e-2325
pallium2.28e-2325
ecto-epithelium8.97e-21104
anatomical cluster5.30e-20373
ectoderm-derived structure5.65e-19171
ectoderm5.65e-19171
presumptive ectoderm5.65e-19171
structure with developmental contribution from neural crest1.09e-18132
multi-tissue structure5.96e-15342
anatomical conduit3.32e-14240
tube1.32e-12192
organ part2.92e-10218
organ3.12e-10503
embryo4.10e-10592
gyrus1.02e-096
multi-cellular organism3.91e-09656
neural nucleus4.41e-099
nucleus of brain4.41e-099
segmental subdivision of hindbrain1.26e-0812
hindbrain1.26e-0812
presumptive hindbrain1.26e-0812
occipital lobe2.27e-085
epithelium2.80e-08306
developing anatomical structure2.97e-08581
embryonic structure3.21e-08564
germ layer3.87e-08560
germ layer / neural crest3.87e-08560
embryonic tissue3.87e-08560
presumptive structure3.87e-08560
germ layer / neural crest derived structure3.87e-08560
epiblast (generic)3.87e-08560
parietal lobe4.57e-085
brainstem4.86e-086
cell layer5.24e-08309
posterior neural tube8.35e-0815
chordal neural plate8.35e-0815
segmental subdivision of nervous system8.83e-0813
male reproductive organ1.65e-0711
temporal lobe3.26e-076
telencephalic nucleus3.34e-077
basal ganglion5.96e-079
nuclear complex of neuraxis5.96e-079
aggregate regional part of brain5.96e-079
collection of basal ganglia5.96e-079
cerebral subcortex5.96e-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
NRF1#4899312.21027944771090.0005492172401020010.00471940919359988



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.