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Coexpression cluster:C3395: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189565756827322!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324265842971023!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139821891881894
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189565756827322!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324265842971023!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139821891881894
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,3.61775,0.855276,0.567465,0.469078,0.598234,1.82956,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,2.41357,1.45054,1.10051,0.414196,0.396746,2.54768,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,3.76231,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,2.35823,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,5.59159,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,3.92523
}}
}}

Revision as of 16:06, 26 November 2012


Full id: C3395_brain_colon_cerebellum_eye_temporal_rectum_diencephalon



Phase1 CAGE Peaks

Hg19::chr14:103988232..103988265,+p@chr14:103988232..103988265
+
Hg19::chr14:103988347..103988399,+p@chr14:103988347..103988399
+
Hg19::chr14:103988435..103988448,+p@chr14:103988435..103988448
+


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 tube1.22e-3156
neural rod1.22e-3156
future spinal cord1.22e-3156
neural keel1.22e-3156
central nervous system1.24e-3181
nervous system2.18e-3189
regional part of nervous system6.63e-3053
regional part of brain6.63e-3053
adult organism8.44e-27114
neural plate1.22e-2682
presumptive neural plate1.22e-2682
neurectoderm4.13e-2686
brain4.44e-2668
future brain4.44e-2668
regional part of forebrain4.88e-2641
forebrain4.88e-2641
anterior neural tube4.88e-2641
future forebrain4.88e-2641
organ system subdivision2.00e-24223
telencephalon2.85e-2434
brain grey matter4.54e-2434
gray matter4.54e-2434
cerebral hemisphere6.62e-2332
regional part of telencephalon9.53e-2332
pre-chordal neural plate5.84e-2161
ecto-epithelium1.30e-20104
ectoderm-derived structure4.06e-20171
ectoderm4.06e-20171
presumptive ectoderm4.06e-20171
cerebral cortex1.00e-1725
pallium1.00e-1725
organ part2.31e-17218
structure with developmental contribution from neural crest6.08e-16132
anatomical cluster1.23e-15373
regional part of cerebral cortex3.05e-1522
neocortex6.60e-1420
multi-tissue structure9.03e-14342
organ3.84e-09503
epithelium3.69e-08306
embryo6.23e-08592
neural nucleus8.51e-089
nucleus of brain8.51e-089
cell layer9.22e-08309
tube1.08e-07192
basal ganglion1.56e-079
nuclear complex of neuraxis1.56e-079
aggregate regional part of brain1.56e-079
collection of basal ganglia1.56e-079
cerebral subcortex1.56e-079
larynx2.42e-079
multi-cellular organism2.72e-07656
anatomical conduit5.45e-07240
posterior neural tube5.59e-0715
chordal neural plate5.59e-0715


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
CCNT2#90536.336201576962630.003930750035764890.0189565756827322
E2F1#186934.907389214879320.008460985347239390.0324265842971023
ZBTB7A#5134137.35190930787590.002516255860282270.0139821891881894



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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