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Coexpression cluster:C1878: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;4:50.1736002714625:3.18412825898083e-07:1.596481859048e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239387532153107!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109105901089242!NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.00136586129314529!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298486432546949
|tf_chipseq_enrich=CTBP2#1488;4:50.1736002714625:3.18412825898083e-07:1.596481859048e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239387532153107!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109105901089242!NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.00136586129314529!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298486432546949
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}}
}}

Revision as of 15:09, 26 November 2012


Full id: C1878_thyroid_aorta_temporal_occipital_throat_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr2:107502615..107502628,-p5@ST6GAL2
Hg19::chr2:107503290..107503348,-p1@ST6GAL2
Hg19::chr2:107503558..107503580,-p8@ST6GAL2
Hg19::chr2:107503727..107503742,-p4@ST6GAL2
Hg19::chr2:107503767..107503775,-p13@ST6GAL2


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
central nervous system3.98e-4481
neural tube2.13e-4156
neural rod2.13e-4156
future spinal cord2.13e-4156
neural keel2.13e-4156
nervous system2.28e-4189
regional part of nervous system1.14e-3953
regional part of brain1.14e-3953
brain3.52e-3668
future brain3.52e-3668
telencephalon1.27e-3334
brain grey matter1.54e-3334
gray matter1.54e-3334
adult organism4.37e-33114
regional part of forebrain5.40e-3341
forebrain5.40e-3341
anterior neural tube5.40e-3341
future forebrain5.40e-3341
cerebral hemisphere2.92e-3132
regional part of telencephalon6.99e-3132
neurectoderm9.94e-3186
neural plate8.93e-3082
presumptive neural plate8.93e-3082
regional part of cerebral cortex1.32e-2422
ecto-epithelium3.26e-24104
organ system subdivision8.15e-24223
ectoderm-derived structure2.83e-23171
ectoderm2.83e-23171
presumptive ectoderm2.83e-23171
pre-chordal neural plate4.67e-2361
cerebral cortex5.47e-2325
pallium5.47e-2325
neocortex6.95e-2220
structure with developmental contribution from neural crest1.06e-21132
anatomical cluster1.32e-14373
tube3.13e-14192
neural nucleus4.14e-129
nucleus of brain4.14e-129
multi-tissue structure1.18e-10342
anatomical conduit1.45e-09240
basal ganglion1.46e-099
nuclear complex of neuraxis1.46e-099
aggregate regional part of brain1.46e-099
collection of basal ganglia1.46e-099
cerebral subcortex1.46e-099
posterior neural tube1.62e-0915
chordal neural plate1.62e-0915
telencephalic nucleus1.84e-097
embryo4.80e-09592
occipital lobe8.75e-095
cell layer1.31e-08309
epithelium1.84e-08306
parietal lobe1.99e-085
embryonic structure5.30e-08564
segmental subdivision of hindbrain6.45e-0812
hindbrain6.45e-0812
presumptive hindbrain6.45e-0812
developing anatomical structure7.96e-08581
germ layer9.60e-08560
germ layer / neural crest9.60e-08560
embryonic tissue9.60e-08560
presumptive structure9.60e-08560
germ layer / neural crest derived structure9.60e-08560
epiblast (generic)9.60e-08560
organ part1.02e-07218
multi-cellular organism2.54e-07656
segmental subdivision of nervous system3.60e-0713
regional part of metencephalon5.63e-079
metencephalon5.63e-079
future metencephalon5.63e-079


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
CTBP2#1488450.17360027146253.18412825898083e-071.596481859048e-05
CTCF#1066444.288205098460020.005152015588243280.0239387532153107
GABPB1#255345.654147068945740.001776696502096670.0109105901089242
NR3C1#2908411.97841866493849.4122920812787e-050.00136586129314529
YY1#752843.928936599883080.007193866269917620.0298486432546949



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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