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Coexpression cluster:C1064

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Full id: C1064_carcinoid_neuroectodermal_amygdala_insula_temporal_frontal_hippocampus



Phase1 CAGE Peaks

Hg19::chr1:20813796..20813807,-p@chr1:20813796..20813807
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Hg19::chr1:20813828..20813867,-p@chr1:20813828..20813867
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Hg19::chr2:119916074..119916122,-p4@C1QL2
Hg19::chr2:119916311..119916368,-p1@C1QL2
Hg19::chr2:119916446..119916455,-p9@C1QL2
Hg19::chr2:119916459..119916470,-p3@C1QL2
Hg19::chr2:119916474..119916485,-p5@C1QL2
Hg19::chr2:119916486..119916506,-p2@C1QL2


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
embryonic stem cell1.32e-105
Uber Anatomy
Ontology termp-valuen
neural tube1.14e-8456
neural rod1.14e-8456
future spinal cord1.14e-8456
neural keel1.14e-8456
regional part of nervous system7.96e-8153
regional part of brain7.96e-8153
telencephalon1.14e-7934
brain grey matter4.17e-7934
gray matter4.17e-7934
regional part of forebrain1.30e-7441
forebrain1.30e-7441
anterior neural tube1.30e-7441
future forebrain1.30e-7441
cerebral hemisphere1.33e-7332
regional part of telencephalon3.78e-7332
regional part of cerebral cortex1.11e-7122
central nervous system3.56e-6881
neocortex1.29e-6420
brain6.78e-6468
future brain6.78e-6468
nervous system1.20e-6389
cerebral cortex1.03e-6225
pallium1.03e-6225
neurectoderm1.10e-6186
neural plate1.46e-6182
presumptive neural plate1.46e-6182
pre-chordal neural plate8.45e-5561
ecto-epithelium3.83e-49104
adult organism2.09e-44114
structure with developmental contribution from neural crest1.08e-38132
ectoderm-derived structure9.54e-36171
ectoderm9.54e-36171
presumptive ectoderm9.54e-36171
organ system subdivision4.53e-22223
gyrus8.18e-226
temporal lobe1.39e-186
limbic system1.59e-185
parietal lobe3.02e-185
tube3.40e-18192
basal ganglion3.64e-189
nuclear complex of neuraxis3.64e-189
aggregate regional part of brain3.64e-189
collection of basal ganglia3.64e-189
cerebral subcortex3.64e-189
occipital lobe1.36e-175
neural nucleus1.49e-179
nucleus of brain1.49e-179
brainstem1.58e-136
anatomical conduit1.04e-12240
posterior neural tube1.55e-1215
chordal neural plate1.55e-1215
telencephalic nucleus4.32e-127
organ part4.59e-12218
frontal cortex9.73e-123
anatomical cluster1.56e-10373
pons1.91e-103
epithelium3.28e-10306
cell layer5.11e-10309
segmental subdivision of hindbrain3.24e-0912
hindbrain3.24e-0912
presumptive hindbrain3.24e-0912
Ammon's horn1.20e-082
lobe parts of cerebral cortex1.20e-082
hippocampal formation1.20e-082
limbic lobe1.20e-082
middle temporal gyrus1.49e-082
corpus striatum1.76e-084
striatum1.76e-084
ventral part of telencephalon1.76e-084
future corpus striatum1.76e-084
segmental subdivision of nervous system1.85e-0813
amygdala2.47e-082
middle frontal gyrus2.96e-082
meninx1.16e-072
membrane organ1.16e-072
meningeal cluster1.16e-072
locus ceruleus1.63e-072
brainstem nucleus1.63e-072
hindbrain nucleus1.63e-072
multi-tissue structure1.64e-07342


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#1066464.020192279806270.0008334820206774180.00628959745357867
EGR1#195853.117611934256340.01051390990388360.0389231943728226
RAD21#588556.47189618466020.0003657753484789720.0036496810566347
SUZ12#23512637.58683568329721.70067604697628e-091.49007471199795e-07



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.