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Coexpression cluster:C3528: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279030152606779!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089650667028565!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436588802828439!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443673528749136
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279030152606779!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089650667028565!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436588802828439!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443673528749136
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,1.99148,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,1.65118,0.242883,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,1.56662,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,4.13274,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,2.54768,2.69227,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,3.56276,1.78371,1.03563,0.624795,1.76124,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:11, 26 November 2012


Full id: C3528_ovary_Endothelial_testis_cervix_uterus_pituitary_spleen



Phase1 CAGE Peaks

Hg19::chr15:95869403..95869412,+p@chr15:95869403..95869412
+
Hg19::chr15:95869424..95869438,+p@chr15:95869424..95869438
+
Hg19::chr15:95869454..95869465,+p@chr15:95869454..95869465
+


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
vein endothelial cell7.14e-096
central nervous system pericyte2.94e-072
Uber Anatomy
Ontology termp-valuen
adult organism5.25e-42114
regional part of nervous system1.62e-1953
regional part of brain1.62e-1953
neural tube3.33e-1856
neural rod3.33e-1856
future spinal cord3.33e-1856
neural keel3.33e-1856
brain1.71e-1568
future brain1.71e-1568
central nervous system4.18e-1581
regional part of forebrain1.01e-1441
forebrain1.01e-1441
anterior neural tube1.01e-1441
future forebrain1.01e-1441
brain grey matter1.42e-1334
gray matter1.42e-1334
nervous system4.88e-1389
neural plate3.42e-1282
presumptive neural plate3.42e-1282
neural nucleus1.65e-119
nucleus of brain1.65e-119
neurectoderm2.19e-1186
regional part of telencephalon1.81e-1032
pre-chordal neural plate4.09e-1061
pons9.98e-103
telencephalon1.00e-0934
vein1.03e-089
venous blood vessel1.03e-089
venous system1.03e-089
cerebral hemisphere1.26e-0832
ecto-epithelium1.52e-08104
brainstem2.34e-086
gland of diencephalon2.63e-084
neuroendocrine gland2.63e-084
basal ganglion3.59e-089
nuclear complex of neuraxis3.59e-089
aggregate regional part of brain3.59e-089
collection of basal ganglia3.59e-089
cerebral subcortex3.59e-089
pituitary gland4.63e-082
structure with developmental contribution from neural crest4.89e-08132
organ system subdivision1.12e-07223
diencephalon1.20e-077
future diencephalon1.20e-077
meninx1.72e-072
membrane organ1.72e-072
meningeal cluster1.72e-072
tube2.13e-07192
locus ceruleus3.67e-072
brainstem nucleus3.67e-072
hindbrain nucleus3.67e-072
regional part of cerebral cortex3.89e-0722
telencephalic nucleus6.00e-077
anatomical cluster6.57e-07373


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
CTCF#1066435.360256373075030.0064925092527670.0279030152606779
FOS#235338.99795530889440.001372499272417130.0089650667028565
GATA2#2624312.7449317335540.0004829527704283790.00436588802828439
JUN#3725312.51282919233630.0005103313992726250.00443673528749136



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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