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Coexpression cluster:C1942: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 17:48, 8 August 2012


Full id: C1942_Neural_spinal_Astrocyte_Neurons_caudate_locus_medial



Phase1 CAGE Peaks

Hg19::chr4:57547751..57547764,-p6@HOPX
Hg19::chr4:57547773..57547780,-p12@HOPX
Hg19::chr4:57547820..57547829,-p8@HOPX
Hg19::chr4:57547870..57547873,-p11@HOPX
Hg19::chr6:111894900..111894919,-p13@TRAF3IP2


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


GO IDGO nameFDR corrected p-value
GO:0043416regulation of skeletal muscle regeneration0.00104792181796774
GO:0051153regulation of striated muscle cell differentiation0.00104792181796774
GO:0043415positive regulation of skeletal muscle regeneration0.00104792181796774
GO:0051149positive regulation of muscle cell differentiation0.00104792181796774
GO:0051155positive regulation of striated muscle cell differentiation0.00104792181796774
GO:0051147regulation of muscle cell differentiation0.0029939301333032
GO:0043403skeletal muscle regeneration0.0029939301333032
GO:0048522positive regulation of cellular process0.00785744710401431
GO:0051146striated muscle cell differentiation0.00785744710401431
GO:0042246tissue regeneration0.00785744710401431
GO:0048518positive regulation of biological process0.00785744710401431
GO:0031099regeneration0.00785744710401431
GO:0048589developmental growth0.0149048318470955
GO:0042692muscle cell differentiation0.0164063264175261
GO:0045597positive regulation of cell differentiation0.0164063264175261
GO:0051094positive regulation of developmental process0.0222463790385095
GO:0014706striated muscle development0.0270879516452688
GO:0007507heart development0.0272617417255358
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0272617417255358
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0282493298120415
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0311397934867029
GO:0042060wound healing0.0311397934867029
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0313714865634195
GO:0045595regulation of cell differentiation0.0313714865634195
GO:0009967positive regulation of signal transduction0.0319946685882814
GO:0007517muscle development0.0345747901444914
GO:0045892negative regulation of transcription, DNA-dependent0.0392769744282824
GO:0016564transcription repressor activity0.0399200397743542
GO:0050793regulation of developmental process0.0424920942631532



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 tube6.09e-6357
neural rod6.09e-6357
future spinal cord6.09e-6357
neural keel6.09e-6357
central nervous system6.99e-6082
regional part of nervous system1.88e-5594
nervous system1.88e-5594
regional part of brain5.64e-5459
brain3.33e-4969
future brain3.33e-4969
adult organism2.83e-48115
regional part of forebrain4.64e-4741
forebrain4.64e-4741
future forebrain4.64e-4741
anterior neural tube1.30e-4542
gray matter1.83e-4434
brain grey matter1.83e-4434
telencephalon3.38e-4434
regional part of telencephalon7.87e-4333
neural plate7.60e-4286
presumptive neural plate7.60e-4286
cerebral hemisphere8.84e-4232
neurectoderm4.26e-3990
cerebral cortex7.90e-3325
pallium7.90e-3325
head2.52e-30123
anterior region of body3.09e-30129
craniocervical region3.09e-30129
pre-chordal neural plate3.92e-3061
regional part of cerebral cortex1.63e-2822
ectoderm-derived structure1.64e-28169
ectoderm2.64e-27173
presumptive ectoderm2.64e-27173
neocortex1.03e-2520
posterior neural tube9.78e-1815
chordal neural plate9.78e-1815
tube3.93e-16194
segmental subdivision of nervous system1.66e-1413
anatomical conduit4.29e-14241
anatomical cluster8.78e-14286
segmental subdivision of hindbrain1.84e-1312
hindbrain1.84e-1312
presumptive hindbrain1.84e-1312
nucleus of brain6.73e-139
neural nucleus6.73e-139
basal ganglion1.01e-129
nuclear complex of neuraxis1.01e-129
aggregate regional part of brain1.01e-129
collection of basal ganglia1.01e-129
cerebral subcortex1.01e-129
epithelium1.67e-10309
organism subdivision2.52e-10365
cell layer3.42e-10312
telencephalic nucleus4.09e-107
organ part1.23e-09219
gyrus1.42e-096
regional part of metencephalon1.62e-099
metencephalon1.62e-099
future metencephalon1.62e-099
temporal lobe2.63e-097
brainstem3.17e-098
limbic system2.83e-085
occipital lobe5.89e-085
parietal lobe6.78e-085
organ1.76e-07511
multi-tissue structure2.05e-07347


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.