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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic
|full_id=C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic
|gostat_on_coexpression_clusters=GO:0043085!positive regulation of catalytic activity!0.00666478581887981!842;79092;8527$GO:0032147!activation of protein kinase activity!0.0144788471296079!79092;8527$GO:0046982!protein heterodimerization activity!0.0159147723705919!7163;8527$GO:0050790!regulation of catalytic activity!0.0159147723705919!842;79092;8527$GO:0065009!regulation of a molecular function!0.0159147723705919!842;79092;8527$GO:0045860!positive regulation of protein kinase activity!0.0159147723705919!79092;8527$GO:0033674!positive regulation of kinase activity!0.0159147723705919!79092;8527$GO:0051347!positive regulation of transferase activity!0.0159147723705919!79092;8527$GO:0042803!protein homodimerization activity!0.0163259198672619!7163;8527$GO:0004035!alkaline phosphatase activity!0.020550845677255!248$GO:0050700!CARD domain binding!0.023967518948923!79092$GO:0045859!regulation of protein kinase activity!0.023967518948923!79092;8527$GO:0043549!regulation of kinase activity!0.023967518948923!79092;8527$GO:0051338!regulation of transferase activity!0.023967518948923!79092;8527$GO:0046339!diacylglycerol metabolic process!0.023967518948923!8527$GO:0008635!caspase activation via cytochrome c!0.0288826181170591!842$GO:0007250!activation of NF-kappaB-inducing kinase!0.0362320546560548!79092$GO:0042802!identical protein binding!0.0404723163106256!7163;8527$GO:0046983!protein dimerization activity!0.0404723163106256!7163;8527
|gostat_on_coexpression_clusters=GO:0043085!positive regulation of catalytic activity!0.00666478581887981!842;79092;8527$GO:0032147!activation of protein kinase activity!0.0144788471296079!79092;8527$GO:0046982!protein heterodimerization activity!0.0159147723705919!7163;8527$GO:0050790!regulation of catalytic activity!0.0159147723705919!842;79092;8527$GO:0065009!regulation of a molecular function!0.0159147723705919!842;79092;8527$GO:0045860!positive regulation of protein kinase activity!0.0159147723705919!79092;8527$GO:0033674!positive regulation of kinase activity!0.0159147723705919!79092;8527$GO:0051347!positive regulation of transferase activity!0.0159147723705919!79092;8527$GO:0042803!protein homodimerization activity!0.0163259198672619!7163;8527$GO:0004035!alkaline phosphatase activity!0.020550845677255!248$GO:0050700!CARD domain binding!0.023967518948923!79092$GO:0045859!regulation of protein kinase activity!0.023967518948923!79092;8527$GO:0043549!regulation of kinase activity!0.023967518948923!79092;8527$GO:0051338!regulation of transferase activity!0.023967518948923!79092;8527$GO:0046339!diacylglycerol metabolic process!0.023967518948923!8527$GO:0008635!caspase activation via cytochrome c!0.0288826181170591!842$GO:0007250!activation of NF-kappaB-inducing kinase!0.0362320546560548!79092$GO:0042802!identical protein binding!0.0404723163106256!7163;8527$GO:0046983!protein dimerization activity!0.0404723163106256!7163;8527

Revision as of 15:39, 12 September 2012


Full id: C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic



Phase1 CAGE Peaks

Hg19::chr10:99550654..99550658,-p@chr10:99550654..99550658
-
Hg19::chr11:72957611..72957646,+p@chr11:72957611..72957646
+
Hg19::chr13:114748246..114748260,-p@chr13:114748246..114748260
-
Hg19::chr16:15596148..15596153,+p7@C16orf45
Hg19::chr17:78152310..78152314,+p10@CARD14
Hg19::chr17:78152323..78152332,+p3@CARD14
Hg19::chr18:33766737..33766750,-p@chr18:33766737..33766750
-
Hg19::chr18:5521372..5521391,-p@chr18:5521372..5521391
-
Hg19::chr1:15850650..15850657,-p9@CASP9
Hg19::chr1:197411581..197411608,+p@chr1:197411581..197411608
+
Hg19::chr1:207326648..207326670,+p@chr1:207326648..207326670
+
Hg19::chr2:233320827..233320853,+p2@ALPI
Hg19::chr2:233320855..233320886,+p1@ALPI
Hg19::chr2:233323059..233323070,+p@chr2:233323059..233323070
+
Hg19::chr2:233324192..233324197,+p@chr2:233324192..233324197
+
Hg19::chr2:234296792..234296806,+p13@DGKD
Hg19::chr2:933319..933328,-p@chr2:933319..933328
-
Hg19::chr2:933356..933367,-p@chr2:933356..933367
-
Hg19::chr4:173883976..173883983,+p@chr4:173883976..173883983
+
Hg19::chr4:173883984..173884005,+p@chr4:173883984..173884005
+
Hg19::chr4:173884006..173884018,+p@chr4:173884006..173884018
+
Hg19::chr4:173884019..173884038,+p@chr4:173884019..173884038
+
Hg19::chr4:173884042..173884047,+p@chr4:173884042..173884047
+
Hg19::chr5:370139..370155,+p@chr5:370139..370155
+
Hg19::chr5:370156..370169,+p@chr5:370156..370169
+
Hg19::chr5:37249149..37249162,+p@chr5:37249149..37249162
+
Hg19::chr5:58571500..58571517,-p1@uc003jsd.1
Hg19::chr6:1111683..1111701,+p@chr6:1111683..1111701
+
Hg19::chr6:134664463..134664474,+p@chr6:134664463..134664474
+
Hg19::chr6:134718844..134718848,+p@chr6:134718844..134718848
+
Hg19::chr6:152084749..152084760,+p@chr6:152084749..152084760
+
Hg19::chr6:152084846..152084856,+p@chr6:152084846..152084856
+
Hg19::chr6:152084870..152084873,+p@chr6:152084870..152084873
+
Hg19::chr6:152084876..152084885,+p@chr6:152084876..152084885
+
Hg19::chr6:152084890..152084896,+p@chr6:152084890..152084896
+
Hg19::chr6:64276121..64276143,-p@chr6:64276121..64276143
-
Hg19::chr6:64276192..64276203,-p@chr6:64276192..64276203
-
Hg19::chr6:87797935..87797943,-p2@CGA
Hg19::chr8:80963618..80963643,-p15@TPD52
Hg19::chr8:80963645..80963656,-p22@TPD52
Hg19::chr8:80963666..80963669,-p37@TPD52
Hg19::chr8:80963673..80963679,-p29@TPD52
Hg19::chrX:2420841..2420865,-p4@DHRSX
Hg19::chrX:2420871..2420883,-p6@DHRSX
Hg19::chrX:57619447..57619495,+p2@ZXDB


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:0043085positive regulation of catalytic activity0.00666478581887981
GO:0032147activation of protein kinase activity0.0144788471296079
GO:0046982protein heterodimerization activity0.0159147723705919
GO:0050790regulation of catalytic activity0.0159147723705919
GO:0065009regulation of a molecular function0.0159147723705919
GO:0045860positive regulation of protein kinase activity0.0159147723705919
GO:0033674positive regulation of kinase activity0.0159147723705919
GO:0051347positive regulation of transferase activity0.0159147723705919
GO:0042803protein homodimerization activity0.0163259198672619
GO:0004035alkaline phosphatase activity0.020550845677255
GO:0050700CARD domain binding0.023967518948923
GO:0045859regulation of protein kinase activity0.023967518948923
GO:0043549regulation of kinase activity0.023967518948923
GO:0051338regulation of transferase activity0.023967518948923
GO:0046339diacylglycerol metabolic process0.023967518948923
GO:0008635caspase activation via cytochrome c0.0288826181170591
GO:0007250activation of NF-kappaB-inducing kinase0.0362320546560548
GO:0042802identical protein binding0.0404723163106256
GO:0046983protein dimerization activity0.0404723163106256



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism3.51e-22115
organ2.01e-16511
multi-cellular organism7.58e-16659
anatomical cluster1.93e-14286
anatomical system7.03e-14625
anatomical group8.73e-14626
digestive system9.38e-14155
digestive tract9.38e-14155
primitive gut9.38e-14155
multi-tissue structure1.76e-13347
subdivision of digestive tract2.54e-13129
endodermal part of digestive tract2.54e-13129
endoderm-derived structure4.84e-13169
endoderm4.84e-13169
presumptive endoderm4.84e-13169
embryo2.71e-11612
mixed endoderm/mesoderm-derived structure3.93e-11130
anatomical conduit1.37e-10241
embryonic structure3.15e-10605
developing anatomical structure3.15e-10605
germ layer5.39e-10604
embryonic tissue5.39e-10604
presumptive structure5.39e-10604
epiblast (generic)5.39e-10604
foregut7.07e-0998
neural tube1.56e-0857
neural rod1.56e-0857
future spinal cord1.56e-0857
neural keel1.56e-0857
tube2.53e-08194
regional part of brain3.85e-0859
endo-epithelium4.00e-0882
central nervous system4.84e-0882
larynx9.48e-089
regional part of forebrain1.64e-0741
forebrain1.64e-0741
future forebrain1.64e-0741
organ part2.31e-07219
brain2.61e-0769
future brain2.61e-0769
regional part of cerebral cortex2.99e-0722
anterior neural tube6.12e-0742
Disease
Ontology termp-valuen
carcinoma1.66e-12106
cell type cancer4.28e-09143


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#1051142.479912594701050.0008753074883893530.00652926496535217
GATA3#262584.842047352392180.0002100809335598130.00244518473420855
NR3C1#290882.661870814430760.009192961431128360.0347674705379546
STAT3#6774122.80519066590780.0007801882787431220.00611268444438506



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

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