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Coexpression cluster:C2315: Difference between revisions

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}}
}}

Revision as of 15:25, 26 November 2012


Full id: C2315_occipital_parietal_temporal_duodenum_medial_brain_putamen



Phase1 CAGE Peaks

Hg19::chr14:78640068..78640069,+p@chr14:78640068..78640069
+
Hg19::chr16:6069184..6069193,+p29@RBFOX1
Hg19::chr16:6550901..6550907,+p@chr16:6550901..6550907
+
Hg19::chr16:7217007..7217010,+p@chr16:7217007..7217010
+


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 tube9.83e-11856
neural rod9.83e-11856
future spinal cord9.83e-11856
neural keel9.83e-11856
regional part of nervous system1.30e-10853
regional part of brain1.30e-10853
central nervous system1.52e-10081
brain9.46e-9468
future brain9.46e-9468
nervous system3.60e-9389
brain grey matter7.41e-8934
gray matter7.41e-8934
telencephalon9.18e-8934
regional part of forebrain9.19e-8841
forebrain9.19e-8841
anterior neural tube9.19e-8841
future forebrain9.19e-8841
neural plate1.78e-8482
presumptive neural plate1.78e-8482
neurectoderm1.44e-8386
cerebral hemisphere5.53e-8332
regional part of telencephalon8.22e-8332
regional part of cerebral cortex1.29e-6922
ecto-epithelium2.08e-64104
pre-chordal neural plate1.83e-6361
neocortex4.46e-6320
cerebral cortex7.12e-6125
pallium7.12e-6125
structure with developmental contribution from neural crest8.05e-51132
adult organism5.29e-50114
ectoderm-derived structure1.44e-47171
ectoderm1.44e-47171
presumptive ectoderm1.44e-47171
organ system subdivision5.03e-37223
basal ganglion7.99e-309
nuclear complex of neuraxis7.99e-309
aggregate regional part of brain7.99e-309
collection of basal ganglia7.99e-309
cerebral subcortex7.99e-309
posterior neural tube3.24e-2915
chordal neural plate3.24e-2915
neural nucleus4.91e-299
nucleus of brain4.91e-299
tube2.05e-28192
telencephalic nucleus3.15e-237
gyrus3.82e-216
segmental subdivision of hindbrain6.17e-2112
hindbrain6.17e-2112
presumptive hindbrain6.17e-2112
anatomical conduit1.57e-20240
anatomical cluster2.54e-19373
segmental subdivision of nervous system3.41e-1913
brainstem3.44e-196
organ part1.28e-18218
temporal lobe3.57e-186
limbic system7.01e-185
parietal lobe8.05e-185
occipital lobe1.65e-175
epithelium1.69e-15306
cell layer3.07e-15309
corpus striatum1.29e-144
striatum1.29e-144
ventral part of telencephalon1.29e-144
future corpus striatum1.29e-144
multi-tissue structure1.89e-13342
regional part of metencephalon6.19e-139
metencephalon6.19e-139
future metencephalon6.19e-139
frontal cortex1.59e-113
caudate-putamen1.90e-113
dorsal striatum1.90e-113
medulla oblongata1.77e-103
myelencephalon1.77e-103
future myelencephalon1.77e-103
pons1.96e-103
spinal cord2.09e-103
dorsal region element2.09e-103
dorsum2.09e-103
germ layer1.06e-08560
germ layer / neural crest1.06e-08560
embryonic tissue1.06e-08560
presumptive structure1.06e-08560
germ layer / neural crest derived structure1.06e-08560
epiblast (generic)1.06e-08560
developing anatomical structure1.47e-08581
embryonic structure1.51e-08564
middle frontal gyrus2.17e-082
middle temporal gyrus2.50e-082
amygdala2.59e-082
embryo3.65e-08592
caudate nucleus3.95e-082
future caudate nucleus3.95e-082
Ammon's horn4.24e-082
lobe parts of cerebral cortex4.24e-082
hippocampal formation4.24e-082
limbic lobe4.24e-082
organ9.58e-08503
globus pallidus1.55e-072
pallidum1.55e-072
locus ceruleus1.65e-072


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

No analysis results for this cluster

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.

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