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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.321756494657324,0.285041334911266,0.258483456842414,0.210041834581101,0.514665628074731,0.390919118470156,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.671850370299825,0.839741672317418,1.02346349500974,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0516025752814806,0.0858366336134482,0,0.115932033194051,0.102851129332916,0.0381808373167472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C130_iPS_HES3GFP_H9_teratocarcinoma_testicular_colon_Alveolar
|full_id=C130_iPS_HES3GFP_H9_teratocarcinoma_testicular_colon_Alveolar
|gostat_on_coexpression_clusters=GO:0032870!cellular response to hormone stimulus!0.0466266336983398!255738$GO:0032869!cellular response to insulin stimulus!0.0466266336983398!255738$GO:0047173!phosphatidylcholine-retinol O-acyltransferase activity!0.0466266336983398!9227$GO:0008326!site-specific DNA-methyltransferase (cytosine-specific) activity!0.0466266336983398!1789
|gostat_on_coexpression_clusters=GO:0032870!cellular response to hormone stimulus!0.0466266336983398!255738$GO:0032869!cellular response to insulin stimulus!0.0466266336983398!255738$GO:0047173!phosphatidylcholine-retinol O-acyltransferase activity!0.0466266336983398!9227$GO:0008326!site-specific DNA-methyltransferase (cytosine-specific) activity!0.0466266336983398!1789

Revision as of 13:50, 12 September 2012


Full id: C130_iPS_HES3GFP_H9_teratocarcinoma_testicular_colon_Alveolar



Phase1 CAGE Peaks

Hg19::chr10:118084968..118084984,+p@chr10:118084968..118084984
+
Hg19::chr10:118085003..118085010,+p@chr10:118085003..118085010
+
Hg19::chr10:13390590..13390601,-p13@SEPHS1
Hg19::chr10:53798976..53798977,-p@chr10:53798976..53798977
-
Hg19::chr10:61899712..61899723,+p@chr10:61899712..61899723
+
Hg19::chr10:6830164..6830166,-p@chr10:6830164..6830166
-
Hg19::chr10:74804784..74804793,-p@chr10:74804784..74804793
-
Hg19::chr10:92567391..92567407,+p@chr10:92567391..92567407
+
Hg19::chr11:131123319..131123338,+p1@ENST00000416553
Hg19::chr11:64016117..64016151,-p@chr11:64016117..64016151
-
Hg19::chr11:64016224..64016227,-p@chr11:64016224..64016227
-
Hg19::chr11:94383510..94383526,+p@chr11:94383510..94383526
+
Hg19::chr11:94383593..94383614,+p@chr11:94383593..94383614
+
Hg19::chr12:11762229..11762247,+p@chr12:11762229..11762247
+
Hg19::chr12:132280681..132280688,+p3@SFSWAP
Hg19::chr12:23738971..23738975,+p@chr12:23738971..23738975
+
Hg19::chr12:6646472..6646496,+p18@GAPDH
Hg19::chr12:7942020..7942031,+p2@NANOG
Hg19::chr12:89346452..89346459,+p@chr12:89346452..89346459
+
Hg19::chr12:9067123..9067159,+p4@PHC1
Hg19::chr12:9067338..9067352,+p9@PHC1
Hg19::chr13:41495638..41495642,+p@chr13:41495638..41495642
+
Hg19::chr13:43438216..43438239,-p@chr13:43438216..43438239
-
Hg19::chr13:51743748..51743762,+p@chr13:51743748..51743762
+
Hg19::chr13:51745257..51745261,+p@chr13:51745257..51745261
+
Hg19::chr14:105634536..105634543,+p@chr14:105634536..105634543
+
Hg19::chr14:21776910..21776928,-p@chr14:21776910..21776928
-
Hg19::chr14:38660185..38660188,+p1@ENST00000555655
Hg19::chr14:84428225..84428229,+p@chr14:84428225..84428229
+
Hg19::chr15:100980707..100980708,+p@chr15:100980707..100980708
+
Hg19::chr15:25219499..25219545,+p7@SNRPN
Hg19::chr15:25223016..25223033,+p@chr15:25223016..25223033
+
Hg19::chr15:40731985..40732002,+p17@BAHD1
Hg19::chr15:41907429..41907432,+p1@ENST00000478625
Hg19::chr15:56363634..56363673,+p@chr15:56363634..56363673
+
Hg19::chr15:56363776..56363799,+p@chr15:56363776..56363799
+
Hg19::chr15:56364190..56364209,+p@chr15:56364190..56364209
+
Hg19::chr15:56364413..56364448,+p@chr15:56364413..56364448
+
Hg19::chr15:56364458..56364485,+p@chr15:56364458..56364485
+
Hg19::chr15:56365001..56365013,+p@chr15:56365001..56365013
+
Hg19::chr15:56365091..56365112,+p@chr15:56365091..56365112
+
Hg19::chr15:56365189..56365204,+p@chr15:56365189..56365204
+
Hg19::chr15:56365882..56365895,+p@chr15:56365882..56365895
+
Hg19::chr15:78635894..78635913,+p@chr15:78635894..78635913
+
Hg19::chr16:29720498..29720506,+p@chr16:29720498..29720506
+
Hg19::chr16:29720511..29720528,+p@chr16:29720511..29720528
+
Hg19::chr16:29740207..29740210,+p@chr16:29740207..29740210
+
Hg19::chr16:3064994..3065011,-p@chr16:3064994..3065011
-
Hg19::chr16:3065277..3065296,-p@chr16:3065277..3065296
-
Hg19::chr16:30876603..30876606,+p@chr16:30876603..30876606
+
Hg19::chr16:69139543..69139585,+p2@HAS3
Hg19::chr16:9761290..9761294,-p@chr16:9761290..9761294
-
Hg19::chr16:9768264..9768287,+p@chr16:9768264..9768287
+
Hg19::chr17:80030062..80030069,+p@chr17:80030062..80030069
+
Hg19::chr19:3028439..3028443,-p@chr19:3028439..3028443
-
Hg19::chr19:33542309..33542310,+p1@ENST00000463585
Hg19::chr19:54335755..54335775,+p@chr19:54335755..54335775
+
Hg19::chr1:114574998..114575000,+p@chr1:114574998..114575000
+
Hg19::chr1:155561105..155561109,-p1@ENST00000427475
Hg19::chr1:18624811..18624839,-p@chr1:18624811..18624839
-
Hg19::chr1:200343233..200343245,-p3@C1orf98
Hg19::chr1:200380793..200380807,+p2@uc010ppi.1
Hg19::chr1:223202511..223202515,-p@chr1:223202511..223202515
-
Hg19::chr1:226076843..226076847,-p2@LEFTY1
Hg19::chr1:232254205..232254216,+p@chr1:232254205..232254216
+
Hg19::chr1:46073030..46073040,-p@chr1:46073030..46073040
-
Hg19::chr1:46073987..46074014,-p@chr1:46073987..46074014
-
Hg19::chr1:55505132..55505142,+p3@PCSK9
Hg19::chr1:63787595..63787617,-p3@ENST00000426393
Hg19::chr20:12735430..12735434,+p@chr20:12735430..12735434
+
Hg19::chr20:12738186..12738216,+p@chr20:12738186..12738216
+
Hg19::chr20:31372591..31372603,+p@chr20:31372591..31372603
+
Hg19::chr20:31374351..31374362,+p@chr20:31374351..31374362
+
Hg19::chr20:31380524..31380554,+p@chr20:31380524..31380554
+
Hg19::chr20:31396411..31396416,+p15@DNMT3B
Hg19::chr20:50399087..50399088,-p@chr20:50399087..50399088
-
Hg19::chr2:188430524..188430535,-p20@TFPI
Hg19::chr2:193404441..193404444,+p@chr2:193404441..193404444
+
Hg19::chr2:202896813..202896824,+p@chr2:202896813..202896824
+
Hg19::chr2:210164412..210164415,+p@chr2:210164412..210164415
+
Hg19::chr2:64479926..64479928,+p@chr2:64479926..64479928
+
Hg19::chr2:77316400..77316420,+p@chr2:77316400..77316420
+
Hg19::chr3:109046043..109046063,-p@chr3:109046043..109046063
-
Hg19::chr3:112140140..112140170,-p@chr3:112140140..112140170
-
Hg19::chr3:162435939..162435944,+p@chr3:162435939..162435944
+
Hg19::chr3:176044846..176044854,-p@chr3:176044846..176044854
-
Hg19::chr3:38527183..38527189,+p@chr3:38527183..38527189
+
Hg19::chr3:46616017..46616032,+p2@TDGF1
Hg19::chr3:46618727..46618745,+p3@TDGF1
Hg19::chr3:54672960..54672982,-p@chr3:54672960..54672982
-
Hg19::chr3:65939393..65939412,+p@chr3:65939393..65939412
+
Hg19::chr4:113566800..113566805,+p@chr4:113566800..113566805
+
Hg19::chr4:113569853..113569862,-p1@ENST00000505215
p1@ENST00000509938
Hg19::chr4:113571661..113571692,-p1@ENST00000510655
Hg19::chr4:113573659..113573683,+p@chr4:113573659..113573683
+
Hg19::chr4:150954096..150954098,+p@chr4:150954096..150954098
+
Hg19::chr4:155665927..155665934,+p4@LRAT
Hg19::chr4:180090669..180090673,-p@chr4:180090669..180090673
-
Hg19::chr4:187163408..187163430,+p@chr4:187163408..187163430
+
Hg19::chr4:187163434..187163439,+p@chr4:187163434..187163439
+
Hg19::chr4:187171657..187171667,+p@chr4:187171657..187171667
+
Hg19::chr4:188918405..188918406,+p@chr4:188918405..188918406
+
Hg19::chr4:379933..379948,+p@chr4:379933..379948
+
Hg19::chr4:57458618..57458624,+p@chr4:57458618..57458624
+
Hg19::chr4:62635359..62635371,-p@chr4:62635359..62635371
-
Hg19::chr5:120035355..120035366,-p@chr5:120035355..120035366
-
Hg19::chr5:123833031..123833035,+p@chr5:123833031..123833035
+
Hg19::chr5:142082957..142082972,+p@chr5:142082957..142082972
+
Hg19::chr5:147248693..147248701,-p@chr5:147248693..147248701
-
Hg19::chr5:80501452..80501465,+p1@RNU5D-1
p1@RNU5E-1
Hg19::chr6:121759714..121759721,+p@chr6:121759714..121759721
+
Hg19::chr6:132224075..132224083,+p@chr6:132224075..132224083
+
Hg19::chr6:132234089..132234094,+p@chr6:132234089..132234094
+
Hg19::chr6:15487707..15487724,+p@chr6:15487707..15487724
+
Hg19::chr6:18759117..18759122,-p@chr6:18759117..18759122
-
Hg19::chr6:33084446..33084462,+p@chr6:33084446..33084462
+
Hg19::chr6:71377348..71377355,+p10@SMAP1
Hg19::chr6:77271226..77271236,+p@chr6:77271226..77271236
+
Hg19::chr7:121715171..121715176,-p@chr7:121715171..121715176
-
Hg19::chr7:138144581..138144590,-p@chr7:138144581..138144590
-
Hg19::chr7:51395308..51395318,+p@chr7:51395308..51395318
+
Hg19::chr7:83090055..83090066,+p@chr7:83090055..83090066
+
Hg19::chr7:89853761..89853768,+p@chr7:89853761..89853768
+
Hg19::chr7:93269596..93269602,+p@chr7:93269596..93269602
+
Hg19::chr7:99986543..99986546,+p@chr7:99986543..99986546
+
Hg19::chr8:115308332..115308341,+p@chr8:115308332..115308341
+
Hg19::chr8:128428066..128428078,+p1@POU5F1B
Hg19::chr8:494169..494176,+p@chr8:494169..494176
+
Hg19::chr8:61852178..61852208,+p@chr8:61852178..61852208
+
Hg19::chr8:72587586..72587591,+p1@ENST00000521131
Hg19::chr8:73958509..73958513,+p@chr8:73958509..73958513
+
Hg19::chr9:12948720..12948724,+p@chr9:12948720..12948724
+
Hg19::chr9:76707423..76707428,+p@chr9:76707423..76707428
+
Hg19::chrX:16141667..16141707,+p1@GRPR
Hg19::chrX:2719421..2719424,-p@chrX:2719421..2719424
-
Hg19::chrX:70288369..70288404,-p3@SNX12
Hg19::chrX:83004216..83004220,-p@chrX:83004216..83004220
-
Hg19::chrX:91359700..91359713,-p1@ENST00000540909
p1@uc004efp.1
Hg19::chrX:91359754..91359757,-p2@ENST00000540909
p2@uc004efp.1


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:0032870cellular response to hormone stimulus0.0466266336983398
GO:0032869cellular response to insulin stimulus0.0466266336983398
GO:0047173phosphatidylcholine-retinol O-acyltransferase activity0.0466266336983398
GO:0008326site-specific DNA-methyltransferase (cytosine-specific) activity0.0466266336983398



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
neural tube1.79e-0857
neural rod1.79e-0857
future spinal cord1.79e-0857
neural keel1.79e-0857
central nervous system3.06e-0882
organ1.24e-07511
anterior neural tube1.93e-0742
gray matter2.45e-0734
brain grey matter2.45e-0734
regional part of forebrain3.71e-0741
forebrain3.71e-0741
future forebrain3.71e-0741
regional part of nervous system5.13e-0794
nervous system5.13e-0794
Disease
Ontology termp-valuen
carcinoma6.47e-17106
cell type cancer2.43e-15143
cancer6.84e-11235
disease of cellular proliferation2.01e-10239


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
NANOG#79923245.049458154994997.33000878949244e-118.06679439373868e-09
POU5F1#54601024.13231665121621.93039694695569e-112.32000836298164e-09
TAF7#6879252.056307446928760.0004233126616163930.00395972692042584



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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