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Coexpression cluster:C4090: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279986445556914!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582179699861113!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107357106622587!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190667597364836
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279986445556914!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582179699861113!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107357106622587!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190667597364836
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,0.63803,0.901413,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,1.78399,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,2.26789,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,7.46293,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,2.54931,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:32, 26 November 2012


Full id: C4090_salivary_Hepatocyte_liver_parotid_submaxillary_tongue_lung



Phase1 CAGE Peaks

Hg19::chr22:25507144..25507210,+p@chr22:25507144..25507210
+
Hg19::chr22:25507901..25507915,+p@chr22:25507901..25507915
+
Hg19::chr22:25507920..25507932,+p@chr22:25507920..25507932
+


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
adult organism1.24e-53114
anatomical cluster3.92e-22373
organ system subdivision1.92e-21223
regional part of nervous system4.96e-2153
regional part of brain4.96e-2153
anatomical conduit8.74e-21240
neural tube9.68e-2156
neural rod9.68e-2156
future spinal cord9.68e-2156
neural keel9.68e-2156
regional part of forebrain1.02e-1941
forebrain1.02e-1941
anterior neural tube1.02e-1941
future forebrain1.02e-1941
neural plate2.49e-1982
presumptive neural plate2.49e-1982
pre-chordal neural plate7.57e-1861
neurectoderm8.62e-1886
brain1.04e-1768
future brain1.04e-1768
central nervous system1.04e-1681
brain grey matter3.45e-1534
gray matter3.45e-1534
multi-tissue structure4.37e-15342
ectoderm-derived structure4.51e-15171
ectoderm4.51e-15171
presumptive ectoderm4.51e-15171
ecto-epithelium6.23e-15104
cerebral hemisphere9.19e-1532
telencephalon9.48e-1534
nervous system8.24e-1489
regional part of telencephalon2.07e-1332
tube5.30e-13192
regional part of cerebral cortex6.17e-1322
organ6.98e-13503
neocortex7.43e-1320
structure with developmental contribution from neural crest6.44e-12132
anatomical system2.91e-11624
anatomical group3.50e-11625
multi-cellular organism5.03e-11656
cerebral cortex7.53e-1125
pallium7.53e-1125
epithelium2.43e-10306
cell layer5.04e-10309
subdivision of digestive tract8.56e-10118
embryo9.16e-10592
developing anatomical structure1.51e-09581
exocrine gland2.80e-0931
exocrine system2.80e-0931
germ layer3.58e-09560
germ layer / neural crest3.58e-09560
embryonic tissue3.58e-09560
presumptive structure3.58e-09560
germ layer / neural crest derived structure3.58e-09560
epiblast (generic)3.58e-09560
gland3.88e-0959
embryonic structure7.18e-09564
saliva-secreting gland8.54e-096
gland of oral region8.54e-096
gland of foregut8.54e-096
oral gland8.54e-096
oral cavity8.54e-096
digestive system1.48e-08145
digestive tract1.48e-08145
primitive gut1.48e-08145
foregut1.54e-0887
endoderm-derived structure1.91e-08160
endoderm1.91e-08160
presumptive endoderm1.91e-08160
organ part2.13e-08218
brainstem2.05e-076
diencephalon8.75e-077
future diencephalon8.75e-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
CTCF#1066435.360256373075030.0064925092527670.0279986445556914
FOXA1#3169311.08141974938550.000734755275698670.00582179699861113
FOXA2#3170324.63046375266526.68983856509345e-050.00107357106622587
USF1#739136.361499277207960.00388404057290560.0190667597364836



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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