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Coexpression cluster:C1574: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;4:50.1736002714625:3.18412825898083e-07:1.59495046158129e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239185346737438!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330250644445881!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388312417841625!FOSL2#2355;3:10.158120362737:0.00188199070341543:0.0110896652603252
|tf_chipseq_enrich=CTBP2#1488;4:50.1736002714625:3.18412825898083e-07:1.59495046158129e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239185346737438!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330250644445881!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388312417841625!FOSL2#2355;3:10.158120362737:0.00188199070341543:0.0110896652603252
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}}
}}

Revision as of 14:58, 26 November 2012


Full id: C1574_salivary_maxillary_extraskeletal_cerebellum_gastric_breast_alveolar



Phase1 CAGE Peaks

Hg19::chr10:21462980..21462991,-p5@NEBL
Hg19::chr10:21462998..21463062,-p1@NEBL
Hg19::chr10:21463141..21463150,-p6@NEBL
Hg19::chr10:21463243..21463279,-p3@NEBL
Hg19::chr10:21463310..21463319,-p8@NEBL


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 tube4.69e-3956
neural rod4.69e-3956
future spinal cord4.69e-3956
neural keel4.69e-3956
regional part of nervous system1.08e-3653
regional part of brain1.08e-3653
adult organism5.99e-34114
neural plate1.57e-2982
presumptive neural plate1.57e-2982
central nervous system4.23e-2981
neurectoderm7.31e-2986
regional part of forebrain1.02e-2841
forebrain1.02e-2841
anterior neural tube1.02e-2841
future forebrain1.02e-2841
brain3.66e-2868
future brain3.66e-2868
nervous system2.43e-2489
brain grey matter1.31e-2334
gray matter1.31e-2334
telencephalon2.12e-2334
ecto-epithelium2.86e-22104
cerebral hemisphere5.22e-2232
regional part of telencephalon7.70e-2232
organ system subdivision5.79e-21223
pre-chordal neural plate5.54e-2061
ectoderm-derived structure7.88e-20171
ectoderm7.88e-20171
presumptive ectoderm7.88e-20171
organ1.30e-18503
structure with developmental contribution from neural crest3.07e-17132
cerebral cortex2.18e-1625
pallium2.18e-1625
regional part of cerebral cortex7.27e-1622
neocortex1.32e-1420
multi-tissue structure2.96e-12342
posterior neural tube2.86e-1115
chordal neural plate2.86e-1115
organ part4.96e-11218
multi-cellular organism7.32e-11656
embryo3.37e-10592
anatomical cluster5.42e-10373
anatomical conduit6.82e-10240
anatomical system7.92e-10624
anatomical group1.04e-09625
segmental subdivision of hindbrain4.48e-0912
hindbrain4.48e-0912
presumptive hindbrain4.48e-0912
neural nucleus8.50e-099
nucleus of brain8.50e-099
developing anatomical structure9.07e-09581
basal ganglion1.11e-089
nuclear complex of neuraxis1.11e-089
aggregate regional part of brain1.11e-089
collection of basal ganglia1.11e-089
cerebral subcortex1.11e-089
tube1.54e-08192
segmental subdivision of nervous system4.80e-0813
germ layer5.06e-08560
germ layer / neural crest5.06e-08560
embryonic tissue5.06e-08560
presumptive structure5.06e-08560
germ layer / neural crest derived structure5.06e-08560
epiblast (generic)5.06e-08560
embryonic structure1.33e-07564
telencephalic nucleus4.96e-077
regional part of metencephalon8.25e-079
metencephalon8.25e-079
future metencephalon8.25e-079
diencephalon9.71e-077
future diencephalon9.71e-077


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-071.59495046158129e-05
CTCF#1066444.288205098460020.005152015588243280.0239185346737438
EGR1#195854.988179094810140.0003237398000590710.00330250644445881
FOS#235358.99795530889441.69470025615156e-050.000388312417841625
FOSL2#2355310.1581203627370.001881990703415430.0110896652603252



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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