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Coexpression cluster:C1605: Difference between revisions

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|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318831209268066!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356840047074653
|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318831209268066!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356840047074653
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,1.15291,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,1.06799,1.42042,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.741483,0.709554,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,2.32461,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,1.80913,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,1.78306,0.35004,0.731946,0.0214572
}}
}}

Revision as of 14:59, 26 November 2012


Full id: C1605_CD4_temporal_occipital_duodenum_Neural_mycosis_medial



Phase1 CAGE Peaks

Hg19::chr11:102341112..102341116,-p51@TMEM123
Hg19::chr7:110721611..110721616,+p@chr7:110721611..110721616
+
Hg19::chr7:110731140..110731155,+p2@LRRN3
Hg19::chr7:110731175..110731191,+p1@LRRN3
Hg19::chr7:110731476..110731516,+p3@LRRN3


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
CD8-positive, alpha-beta T cell8.65e-0811
Uber Anatomy
Ontology termp-valuen
neural tube4.83e-5256
neural rod4.83e-5256
future spinal cord4.83e-5256
neural keel4.83e-5256
regional part of nervous system3.69e-5153
regional part of brain3.69e-5153
regional part of forebrain1.97e-4441
forebrain1.97e-4441
anterior neural tube1.97e-4441
future forebrain1.97e-4441
brain grey matter1.99e-4234
gray matter1.99e-4234
telencephalon5.09e-4234
cerebral hemisphere1.18e-4032
regional part of telencephalon2.87e-4032
central nervous system2.21e-3981
nervous system1.23e-3789
brain2.54e-3768
future brain2.54e-3768
neural plate2.63e-3582
presumptive neural plate2.63e-3582
neurectoderm3.74e-3486
cerebral cortex1.01e-3125
pallium1.01e-3125
adult organism9.08e-30114
pre-chordal neural plate1.80e-2961
regional part of cerebral cortex2.48e-2922
neocortex3.38e-2720
ecto-epithelium2.45e-26104
structure with developmental contribution from neural crest3.45e-20132
ectoderm-derived structure5.36e-20171
ectoderm5.36e-20171
presumptive ectoderm5.36e-20171
organ system subdivision2.27e-18223
basal ganglion2.04e-129
nuclear complex of neuraxis2.04e-129
aggregate regional part of brain2.04e-129
collection of basal ganglia2.04e-129
cerebral subcortex2.04e-129
neural nucleus5.50e-129
nucleus of brain5.50e-129
temporal lobe3.63e-106
telencephalic nucleus6.34e-107
posterior neural tube2.77e-0915
chordal neural plate2.77e-0915
gyrus7.38e-096
segmental subdivision of hindbrain2.84e-0812
hindbrain2.84e-0812
presumptive hindbrain2.84e-0812
brainstem4.92e-086
anatomical cluster6.79e-08373
occipital lobe9.33e-085
segmental subdivision of nervous system1.84e-0713
limbic system2.17e-075
parietal lobe2.29e-075
tube3.32e-07192


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
RAD21#588536.21302033727380.007751055068811640.0318831209268066
REST#597835.790017229676810.009468788694433940.0356840047074653



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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