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Coexpression cluster:C2883

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Full id: C2883_carcinosarcoma_gastrointestinal_nonsmall_amygdala_frontal_occipital_pineal



Phase1 CAGE Peaks

Hg19::chr7:145813151..145813164,+p14@CNTNAP2
Hg19::chr7:145813700..145813711,+p15@CNTNAP2
Hg19::chr7:145813717..145813743,+p5@CNTNAP2
Hg19::chr7:145813864..145813947,+p1@CNTNAP2


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
central nervous system9.57e-5482
regional part of nervous system3.49e-5394
nervous system3.49e-5394
neural tube2.46e-4957
neural rod2.46e-4957
future spinal cord2.46e-4957
neural keel2.46e-4957
regional part of brain1.22e-4759
brain3.30e-4769
future brain3.30e-4769
neurectoderm5.92e-4390
neural plate8.62e-4286
presumptive neural plate8.62e-4286
anterior region of body2.94e-40129
craniocervical region2.94e-40129
head1.39e-39123
ectoderm5.80e-38173
presumptive ectoderm5.80e-38173
regional part of forebrain6.12e-3841
forebrain6.12e-3841
future forebrain6.12e-3841
anterior neural tube1.30e-3642
ectoderm-derived structure1.30e-36169
gray matter6.54e-3234
brain grey matter6.54e-3234
telencephalon7.01e-3234
regional part of telencephalon7.71e-3133
cerebral hemisphere9.72e-3132
pre-chordal neural plate3.03e-3061
cerebral cortex1.21e-2425
pallium1.21e-2425
regional part of cerebral cortex7.93e-2422
adult organism1.81e-23115
neocortex5.59e-2220
posterior neural tube1.96e-1315
chordal neural plate1.96e-1315
organism subdivision4.96e-13365
segmental subdivision of nervous system8.97e-1213
segmental subdivision of hindbrain4.38e-1112
hindbrain4.38e-1112
presumptive hindbrain4.38e-1112
temporal lobe5.41e-097
basal ganglion6.71e-099
nuclear complex of neuraxis6.71e-099
aggregate regional part of brain6.71e-099
collection of basal ganglia6.71e-099
cerebral subcortex6.71e-099
multi-tissue structure1.03e-08347
organ part1.12e-08219
nucleus of brain1.14e-089
neural nucleus1.14e-089
tube1.40e-08194
regional part of metencephalon1.43e-089
metencephalon1.43e-089
future metencephalon1.43e-089
anatomical cluster2.83e-08286
organ3.08e-08511
gyrus1.30e-076
diencephalon2.18e-077
future diencephalon2.18e-077
anatomical conduit2.45e-07241
multi-cellular organism4.25e-07659
telencephalic nucleus6.46e-077


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
REST#597837.237521537096020.004104697304192610.0195972791658318



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.