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Coexpression cluster:C1485: Difference between revisions

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|tf_chipseq_enrich=PAX5#5079;6:6.66956553117783:1.13557256338955e-05:0.000289970814053401!REST#5978;6:9.65002871612802:1.23743801704917e-06:4.99176473783695e-05!SIN3A#25942;6:5.40888472681514:3.99207083571449e-05:0.000743186962586783!SUZ12#23512;6:50.1157809110629:6.2866744827465e-11:6.99226833124134e-09
|tf_chipseq_enrich=PAX5#5079;6:6.66956553117783:1.13557256338955e-05:0.000289970814053401!REST#5978;6:9.65002871612802:1.23743801704917e-06:4.99176473783695e-05!SIN3A#25942;6:5.40888472681514:3.99207083571449e-05:0.000743186962586783!SUZ12#23512;6:50.1157809110629:6.2866744827465e-11:6.99226833124134e-09
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}}
}}

Revision as of 14:55, 26 November 2012


Full id: C1485_myeloma_putamen_caudate_nucleus_Dendritic_pons_Lymphatic



Phase1 CAGE Peaks

Hg19::chr20:9495321..9495340,+p8@LAMP5
Hg19::chr20:9495383..9495390,+p14@LAMP5
Hg19::chr20:9495392..9495403,+p9@LAMP5
Hg19::chr20:9495410..9495426,+p5@LAMP5
Hg19::chr20:9495430..9495472,+p2@LAMP5
Hg19::chr20:9495486..9495495,+p13@LAMP5


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
plasmacytoid dendritic cell5.35e-073
Uber Anatomy
Ontology termp-valuen
neural tube6.21e-6156
neural rod6.21e-6156
future spinal cord6.21e-6156
neural keel6.21e-6156
central nervous system6.42e-5781
regional part of nervous system2.10e-5653
regional part of brain2.10e-5653
nervous system4.93e-5489
brain1.68e-4868
future brain1.68e-4868
regional part of forebrain1.24e-4441
forebrain1.24e-4441
anterior neural tube1.24e-4441
future forebrain1.24e-4441
neural plate6.54e-4482
presumptive neural plate6.54e-4482
adult organism7.54e-42114
neurectoderm4.12e-4186
telencephalon3.49e-4034
brain grey matter4.96e-4034
gray matter4.96e-4034
cerebral hemisphere7.76e-3832
regional part of telencephalon2.22e-3732
pre-chordal neural plate1.49e-3161
ecto-epithelium3.34e-31104
regional part of cerebral cortex1.11e-3022
neocortex1.72e-2720
ectoderm-derived structure1.60e-26171
ectoderm1.60e-26171
presumptive ectoderm1.60e-26171
cerebral cortex2.51e-2625
pallium2.51e-2625
structure with developmental contribution from neural crest1.25e-25132
organ system subdivision4.25e-23223
posterior neural tube9.11e-1715
chordal neural plate9.11e-1715
basal ganglion3.54e-169
nuclear complex of neuraxis3.54e-169
aggregate regional part of brain3.54e-169
collection of basal ganglia3.54e-169
cerebral subcortex3.54e-169
neural nucleus1.85e-159
nucleus of brain1.85e-159
anatomical cluster3.18e-13373
telencephalic nucleus6.37e-137
segmental subdivision of hindbrain1.42e-1212
hindbrain1.42e-1212
presumptive hindbrain1.42e-1212
segmental subdivision of nervous system2.03e-1113
tube2.44e-11192
anatomical conduit3.25e-11240
gyrus6.15e-116
brainstem1.18e-106
limbic system6.89e-105
parietal lobe2.32e-095
temporal lobe2.73e-096
corpus striatum7.90e-094
striatum7.90e-094
ventral part of telencephalon7.90e-094
future corpus striatum7.90e-094
regional part of metencephalon3.00e-089
metencephalon3.00e-089
future metencephalon3.00e-089
caudate-putamen4.87e-073
dorsal striatum4.87e-073


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
PAX5#507966.669565531177831.13557256338955e-050.000289970814053401
REST#597869.650028716128021.23743801704917e-064.99176473783695e-05
SIN3A#2594265.408884726815143.99207083571449e-050.000743186962586783
SUZ12#23512650.11578091106296.2866744827465e-116.99226833124134e-09



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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