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Coexpression cluster:C2806: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 14:26, 19 October 2012


Full id: C2806_occipital_parietal_duodenum_temporal_nonsmall_small_merkel



Phase1 CAGE Peaks

Hg19::chr5:140227945..140227976,+p1@PCDHA9
Hg19::chr6:124125170..124125204,+p3@NKAIN2
Hg19::chr6:124125310..124125362,+p1@NKAIN2
Hg19::chr6:124125374..124125386,+p9@NKAIN2


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 tube9.46e-6756
neural rod9.46e-6756
future spinal cord9.46e-6756
neural keel9.46e-6756
central nervous system7.23e-6281
regional part of nervous system1.17e-6153
regional part of brain1.17e-6153
nervous system2.59e-6089
neurectoderm6.91e-5386
brain7.38e-5168
future brain7.38e-5168
regional part of forebrain8.59e-4941
forebrain8.59e-4941
anterior neural tube8.59e-4941
future forebrain8.59e-4941
neural plate3.01e-4882
presumptive neural plate3.01e-4882
adult organism7.84e-48114
telencephalon1.55e-4434
brain grey matter3.58e-4434
gray matter3.58e-4434
cerebral hemisphere2.34e-4132
regional part of telencephalon2.52e-4132
ecto-epithelium2.86e-39104
ectoderm-derived structure4.17e-38171
ectoderm4.17e-38171
presumptive ectoderm4.17e-38171
pre-chordal neural plate1.09e-3461
regional part of cerebral cortex1.37e-3322
cerebral cortex2.18e-3125
pallium2.18e-3125
neocortex1.02e-3020
structure with developmental contribution from neural crest2.26e-29132
organ system subdivision9.91e-28223
posterior neural tube2.70e-1815
chordal neural plate2.70e-1815
segmental subdivision of nervous system3.27e-1513
neural nucleus4.07e-149
nucleus of brain4.07e-149
basal ganglion4.13e-149
nuclear complex of neuraxis4.13e-149
aggregate regional part of brain4.13e-149
collection of basal ganglia4.13e-149
cerebral subcortex4.13e-149
tube4.83e-14192
segmental subdivision of hindbrain1.40e-1312
hindbrain1.40e-1312
presumptive hindbrain1.40e-1312
anatomical cluster1.45e-12373
telencephalic nucleus2.27e-117
gyrus8.17e-116
anatomical conduit9.20e-11240
brainstem1.27e-106
organ part2.19e-10218
parietal lobe1.74e-095
occipital lobe2.07e-095
regional part of metencephalon3.41e-099
metencephalon3.41e-099
future metencephalon3.41e-099
temporal lobe4.20e-096
limbic system1.20e-085
epithelium8.09e-08306
cell layer1.38e-07309
multi-tissue structure2.21e-07342
corpus striatum4.11e-074
striatum4.11e-074
ventral part of telencephalon4.11e-074
future corpus striatum4.11e-074


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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