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Coexpression cluster:C3969: Difference between revisions

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|tf_chipseq_enrich=TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614275190433915
|tf_chipseq_enrich=TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614275190433915
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0993,0.0440463,2.58765e-05,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.0017212,0.0750181
|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.78451,0.795576,1.21459,0.534793,1.95911,0.599922,1.36391,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,1.60305,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,2.51002,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,1.42224
}}
}}

Revision as of 16:28, 26 November 2012


Full id: C3969_Prostate_Keratinocyte_liver_Small_Tracheal_Hepatocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr1:31907100..31907130,+p@chr1:31907100..31907130
+
Hg19::chr1:31907140..31907157,+p@chr1:31907140..31907157
+
Hg19::chr1:31907237..31907260,+p@chr1:31907237..31907260
+


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
endo-epithelial cell5.78e-1342
endodermal cell8.38e-1358
epithelial cell2.12e-12253
respiratory epithelial cell1.93e-0913
ecto-epithelial cell2.38e-0934
embryonic cell2.57e-09250
general ecto-epithelial cell7.10e-0914
somatic cell9.08e-07588
Uber Anatomy
Ontology termp-valuen
surface structure6.61e-1999
endoderm-derived structure7.52e-19160
endoderm7.52e-19160
presumptive endoderm7.52e-19160
organism subdivision1.05e-15264
orifice2.24e-1436
digestive system1.43e-13145
digestive tract1.43e-13145
primitive gut1.43e-13145
renal system9.88e-1248
urinary system structure3.61e-1147
mouth mucosa2.06e-1013
organ component layer2.67e-1066
mouth1.18e-0929
stomodeum1.18e-0929
cloaca8.97e-0914
anal region8.97e-0914
embryonic cloaca8.97e-0914
terminal part of digestive tract8.97e-0914
primitive urogenital sinus8.97e-0914
proctodeum8.97e-0914
anterior region of body1.09e-0862
craniocervical region1.09e-0862
head1.35e-0856
subdivision of head1.91e-0849
mucosa2.09e-0820
subdivision of digestive tract2.36e-08118
trunk2.77e-08199
mixed endoderm/mesoderm-derived structure2.78e-0829
respiratory system3.01e-0874
genitourinary system6.59e-0815
sex gland1.09e-0712
male reproductive gland1.09e-0712
oral opening2.08e-0722
gingiva3.08e-078
epithelial bud3.32e-0737
endo-epithelium6.33e-0782
chorion7.51e-077
multi-cellular organism7.63e-07656
prostate gland8.19e-0711
male accessory sex gland8.19e-0711
embryonic cloacal epithelium8.19e-0711
epithelium of hindgut8.19e-0711
urogenital sinus epithelium8.19e-0711
prostate bud8.19e-0711
prostate field8.19e-0711


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
TCF7L2#6934310.77017656313730.0008003181298398380.00614275190433915



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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