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Coexpression cluster:C1469: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0046874!quinolinate metabolic process!0.00141292829388908!130013$GO:0001760!aminocarboxymuconate-semialdehyde decarboxylase activity!0.00141292829388908!130013$GO:0004305!ethanolamine kinase activity!0.00211926766548736!55224$GO:0004103!choline kinase activity!0.00211926766548736!55224$GO:0043648!dicarboxylic acid metabolic process!0.00903874877915148!130013$GO:0016831!carboxy-lyase activity!0.0263319827971826!130013$GO:0016830!carbon-carbon lyase activity!0.0330240233239064!130013
|gostat_on_coexpression_clusters=GO:0046874!quinolinate metabolic process!0.00141292829388908!130013$GO:0001760!aminocarboxymuconate-semialdehyde decarboxylase activity!0.00141292829388908!130013$GO:0004305!ethanolamine kinase activity!0.00211926766548736!55224$GO:0004103!choline kinase activity!0.00211926766548736!55224$GO:0043648!dicarboxylic acid metabolic process!0.00903874877915148!130013$GO:0016831!carboxy-lyase activity!0.0263319827971826!130013$GO:0016830!carbon-carbon lyase activity!0.0330240233239064!130013
|id=C1469
|id=C1469
|ontology_enrichment_celltype=CL:0000066!7.10e-10!254;CL:0000223!1.77e-07!59
|ontology_enrichment_celltype=CL:0000349!9.00e-12!19;CL:0002577!9.73e-08!3;CL:0002603!7.92e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.33e-12!365;UBERON:0000062!4.01e-10!511;UBERON:0004119!3.02e-09!169;UBERON:0000925!3.02e-09!169;UBERON:0006595!3.02e-09!169;UBERON:0000077!3.16e-09!130;UBERON:0000481!3.81e-09!347;UBERON:0004921!7.33e-09!129;UBERON:0004185!7.33e-09!129;UBERON:0000468!1.43e-08!659;UBERON:0001007!1.79e-08!155;UBERON:0001555!1.79e-08!155;UBERON:0007026!1.79e-08!155;UBERON:0000466!2.93e-08!126;UBERON:0005177!4.16e-08!107;UBERON:0007023!7.76e-08!115;UBERON:0009569!8.60e-08!113;UBERON:0002530!1.00e-07!59;UBERON:0005631!1.37e-07!14;UBERON:0000158!1.37e-07!14;UBERON:0005172!2.07e-07!55;UBERON:0005173!2.07e-07!55;UBERON:0000064!2.95e-07!219;UBERON:0000153!3.66e-07!129;UBERON:0007811!3.66e-07!129;UBERON:0005911!3.85e-07!82;UBERON:0003929!6.47e-07!54;UBERON:0002417!7.09e-07!61;UBERON:0000916!7.09e-07!61;UBERON:0004121!8.85e-07!169
|ontology_enrichment_uberon=UBERON:0005631!4.54e-14!14;UBERON:0000158!4.54e-14!14;UBERON:0005172!4.12e-10!54;UBERON:0005173!4.12e-10!54;UBERON:0002530!1.35e-09!59;UBERON:0005156!1.39e-09!59;UBERON:0000990!1.39e-09!59;UBERON:0004119!1.43e-09!160;UBERON:0000925!1.43e-09!160;UBERON:0006595!1.43e-09!160;UBERON:0003101!6.54e-09!22;UBERON:0000079!6.54e-09!22;UBERON:0000478!9.65e-09!24;UBERON:0003135!1.07e-08!11;UBERON:0004921!1.26e-08!118;UBERON:0002417!1.41e-08!60;UBERON:0000916!1.41e-08!60;UBERON:0001007!1.82e-08!145;UBERON:0001555!1.82e-08!145;UBERON:0007026!1.82e-08!145;UBERON:0003133!3.76e-08!48;UBERON:0000062!3.83e-08!503;UBERON:0006554!4.18e-08!47;UBERON:0000305!4.59e-08!7;UBERON:0005177!4.82e-08!101;UBERON:0001008!7.52e-08!48;UBERON:0007023!7.66e-08!114;UBERON:0002107!9.05e-08!19;UBERON:0006925!9.05e-08!19;UBERON:0008836!9.05e-08!19;UBERON:0003124!1.26e-07!7;UBERON:0002365!1.63e-07!31;UBERON:0002330!1.63e-07!31;UBERON:0003929!2.01e-07!54;UBERON:0000077!2.35e-07!29;UBERON:0011216!4.89e-07!223;UBERON:0004871!5.59e-07!8;UBERON:0000466!5.83e-07!117;UBERON:0002368!6.90e-07!35;UBERON:0004733!8.03e-07!12;UBERON:0002028!8.03e-07!12;UBERON:0007277!8.03e-07!12
|pathway_enrichment=6.31961929821581e-05;0.0400031901577061;3;1138;Metabolic pathways (KEGG):01100
|pathway_enrichment=6.31961929821581e-05;0.0400031901577061;3;1138;Metabolic pathways (KEGG):01100
|tf_chipseq_enrich=CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159811502354993!NR3C1#2908;4:9.98201555411536:0.000267321918040192:0.00286082936757861!ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.0194891721299022
|tf_chipseq_enrich=CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159811502354993!NR3C1#2908;4:9.98201555411536:0.000267321918040192:0.00286082936757861!ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.0194891721299022
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}}
}}

Revision as of 11:19, 19 October 2012


Full id: C1469_kidney_amniotic_liver_Hepatocyte_Placental_Amniotic_tongue



Phase1 CAGE Peaks

Hg19::chr1:204120903..204120917,-p6@ETNK2
Hg19::chr1:204120920..204120929,-p12@ETNK2
Hg19::chr1:204120931..204120942,-p10@ETNK2
Hg19::chr1:204120945..204120958,-p11@ETNK2
Hg19::chr1:47603109..47603120,+p1@CYP4A22
Hg19::chr2:135595876..135595891,+p3@ACMSD


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


p.valueFDRnGenesnPathwayName
6.31961929821581e-050.040003190157706131138Metabolic pathways (KEGG):01100



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:0046874quinolinate metabolic process0.00141292829388908
GO:0001760aminocarboxymuconate-semialdehyde decarboxylase activity0.00141292829388908
GO:0004305ethanolamine kinase activity0.00211926766548736
GO:0004103choline kinase activity0.00211926766548736
GO:0043648dicarboxylic acid metabolic process0.00903874877915148
GO:0016831carboxy-lyase activity0.0263319827971826
GO:0016830carbon-carbon lyase activity0.0330240233239064



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
extraembryonic cell9.00e-1219
placental epithelial cell9.73e-083
astrocyte of the cerebellum7.92e-073
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane4.54e-1414
membranous layer4.54e-1414
abdomen element4.12e-1054
abdominal segment element4.12e-1054
gland1.35e-0959
reproductive structure1.39e-0959
reproductive system1.39e-0959
endoderm-derived structure1.43e-09160
endoderm1.43e-09160
presumptive endoderm1.43e-09160
male organism6.54e-0922
male reproductive system6.54e-0922
extraembryonic structure9.65e-0924
male reproductive organ1.07e-0811
subdivision of digestive tract1.26e-08118
abdominal segment of trunk1.41e-0860
abdomen1.41e-0860
digestive system1.82e-08145
digestive tract1.82e-08145
primitive gut1.82e-08145
reproductive organ3.76e-0848
organ3.83e-08503
urinary system structure4.18e-0847
amnion4.59e-087
trunk region element4.82e-08101
renal system7.52e-0848
adult organism7.66e-08114
liver9.05e-0819
digestive gland9.05e-0819
liver bud9.05e-0819
chorion1.26e-077
exocrine gland1.63e-0731
exocrine system1.63e-0731
gut epithelium2.01e-0754
mixed endoderm/mesoderm-derived structure2.35e-0729
organ system subdivision4.89e-07223
somatic layer of lateral plate mesoderm5.59e-078
immaterial anatomical entity5.83e-07117
endocrine gland6.90e-0735
segmental subdivision of hindbrain8.03e-0712
hindbrain8.03e-0712
presumptive hindbrain8.03e-0712


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
CEBPB#105145.314098417216540.003008047293917460.0159811502354993
NR3C1#290849.982015554115360.0002673219180401920.00286082936757861
ZBTB7A#5134144.901272871917260.004079628118843750.0194891721299022



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.