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Coexpression cluster:C225: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0019002!GMP binding!0.00809371024079062!10846$GO:0030553!cGMP binding!0.00809371024079062!10846$GO:0030551!cyclic nucleotide binding!0.0122606700313062!10846$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0138255559698253!10846$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0138255559698253!10846$GO:0008081!phosphoric diester hydrolase activity!0.0337831481914176!10846
|gostat_on_coexpression_clusters=GO:0019002!GMP binding!0.00809371024079062!10846$GO:0030553!cGMP binding!0.00809371024079062!10846$GO:0030551!cyclic nucleotide binding!0.0122606700313062!10846$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0138255559698253!10846$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0138255559698253!10846$GO:0008081!phosphoric diester hydrolase activity!0.0337831481914176!10846
|id=C225
|id=C225
|ontology_enrichment_celltype=CL:0000066!6.46e-30!254;CL:0000220!1.86e-13!246;CL:0002321!4.09e-13!248;CL:0002076!2.97e-12!43;CL:0000076!9.20e-11!62;CL:0000223!3.39e-10!59;CL:0002139!6.35e-10!24;CL:0000071!1.94e-07!18;CL:0002546!1.94e-07!18;CL:0000115!2.21e-07!35;CL:0002368!2.32e-07!13;CL:0002078!4.42e-07!44
|ontology_enrichment_disease=DOID:0050687!1.20e-07!143
|ontology_enrichment_uberon=UBERON:0000119!1.29e-07!312;UBERON:0001986!1.94e-07!18;UBERON:0004638!1.94e-07!18;UBERON:0004852!1.94e-07!18;UBERON:0000487!2.41e-07!22;UBERON:0000483!4.29e-07!309;UBERON:0000467!8.00e-07!625
}}
}}

Revision as of 14:21, 21 May 2012


Full id: C225_ductal_alveolar_giant_prostate_salivary_squamous_Tracheal



Phase1 CAGE Peaks

Hg19::chr10:16932413..16932437,-p@chr10:16932413..16932437
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Hg19::chr10:17070392..17070407,-p@chr10:17070392..17070407
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Hg19::chr10:4806777..4806787,-p@chr10:4806777..4806787
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Hg19::chr10:4808676..4808703,-p@chr10:4808676..4808703
-
Hg19::chr10:4808737..4808750,-p@chr10:4808737..4808750
-
Hg19::chr11:13895146..13895156,+p@chr11:13895146..13895156
+
Hg19::chr12:76220619..76220626,-p@chr12:76220619..76220626
-
Hg19::chr13:63967430..63967434,+p@chr13:63967430..63967434
+
Hg19::chr15:35795980..35795985,-p@chr15:35795980..35795985
-
Hg19::chr15:35796430..35796456,-p@chr15:35796430..35796456
-
Hg19::chr17:66818826..66818835,+p@chr17:66818826..66818835
+
Hg19::chr18:2409216..2409225,-p@chr18:2409216..2409225
-
Hg19::chr1:162724324..162724330,+p@chr1:162724324..162724330
+
Hg19::chr1:162825560..162825574,-p1@C1orf110
Hg19::chr1:163063326..163063330,+p@chr1:163063326..163063330
+
Hg19::chr1:78001338..78001348,+p@chr1:78001338..78001348
+
Hg19::chr1:94240786..94240801,-p3@uc001dqd.1
Hg19::chr1:94240846..94240855,-p5@uc001dqd.1
Hg19::chr1:94240877..94240925,-p2@uc001dqd.1
Hg19::chr1:98779728..98779733,-p@chr1:98779728..98779733
-
Hg19::chr1:98850479..98850511,-p@chr1:98850479..98850511
-
Hg19::chr2:114004369..114004400,-p@chr2:114004369..114004400
-
Hg19::chr2:114004420..114004422,-p@chr2:114004420..114004422
-
Hg19::chr2:139757287..139757309,+p@chr2:139757287..139757309
+
Hg19::chr2:139791188..139791193,+p@chr2:139791188..139791193
+
Hg19::chr2:139791209..139791219,+p@chr2:139791209..139791219
+
Hg19::chr2:139791292..139791303,+p@chr2:139791292..139791303
+
Hg19::chr2:196278203..196278206,+p@chr2:196278203..196278206
+
Hg19::chr2:196278365..196278367,+p@chr2:196278365..196278367
+
Hg19::chr2:230450858..230450884,-p@chr2:230450858..230450884
-
Hg19::chr2:230450887..230450899,-p@chr2:230450887..230450899
-
Hg19::chr2:230680106..230680124,-p@chr2:230680106..230680124
-
Hg19::chr2:238378261..238378264,-p@chr2:238378261..238378264
-
Hg19::chr3:149051194..149051242,-p5@TM4SF18
Hg19::chr3:153599269..153599304,+p1@ENST00000463297
Hg19::chr3:188993877..188993894,+p@chr3:188993877..188993894
+
Hg19::chr3:189028187..189028196,+p@chr3:189028187..189028196
+
Hg19::chr3:189030852..189030859,+p@chr3:189030852..189030859
+
Hg19::chr3:189121193..189121200,+p@chr3:189121193..189121200
+
Hg19::chr3:189128229..189128239,+p@chr3:189128229..189128239
+
Hg19::chr3:189151408..189151415,+p@chr3:189151408..189151415
+
Hg19::chr3:83659759..83659783,-p@chr3:83659759..83659783
-
Hg19::chr3:84017708..84017724,+p@chr3:84017708..84017724
+
Hg19::chr4:125901946..125901955,+p@chr4:125901946..125901955
+
Hg19::chr4:81139190..81139200,-p@chr4:81139190..81139200
-
Hg19::chr4:81224883..81224888,+p@chr4:81224883..81224888
+
Hg19::chr5:141766141..141766182,+p@chr5:141766141..141766182
+
Hg19::chr5:27707663..27707672,+p@chr5:27707663..27707672
+
Hg19::chr5:27707697..27707707,+p@chr5:27707697..27707707
+
Hg19::chr5:56589068..56589074,-p@chr5:56589068..56589074
-
Hg19::chr5:56598008..56598013,-p@chr5:56598008..56598013
-
Hg19::chr5:57529651..57529657,+p@chr5:57529651..57529657
+
Hg19::chr5:57529696..57529706,+p@chr5:57529696..57529706
+
Hg19::chr5:57529719..57529726,+p@chr5:57529719..57529726
+
Hg19::chr5:92489155..92489169,-p@chr5:92489155..92489169
-
Hg19::chr6:145247788..145247818,-p@chr6:145247788..145247818
-
Hg19::chr6:165990105..165990115,-p10@PDE10A
Hg19::chr6:165990158..165990169,-p12@PDE10A
Hg19::chr6:169691363..169691375,-p@chr6:169691363..169691375
-
Hg19::chr8:41052616..41052617,-p@chr8:41052616..41052617
-
Hg19::chr8:41053290..41053297,-p@chr8:41053290..41053297
-
Hg19::chrX:13321104..13321106,-p@chrX:13321104..13321106
-
Hg19::chrX:18889509..18889513,+p@chrX:18889509..18889513
+


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

GO IDGO nameFDR corrected p-value
GO:0019002GMP binding0.00809371024079062
GO:0030553cGMP binding0.00809371024079062
GO:0030551cyclic nucleotide binding0.0122606700313062
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0008081phosphoric diester hydrolase activity0.0337831481914176



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
cell layer1.29e-07312
endothelium1.94e-0718
blood vessel endothelium1.94e-0718
cardiovascular system endothelium1.94e-0718
simple squamous epithelium2.41e-0722
epithelium4.29e-07309
anatomical system8.00e-07625
Disease
Ontology termp-valuen
cell type cancer1.20e-07143


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

No analysis results for this cluster

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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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