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Coexpression cluster:C137: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:40, 17 September 2013


Full id: C137_large_ductal_melanoma_cervical_Endothelial_Smooth_chronic



Phase1 CAGE Peaks

Hg19::chr11:17555398..17555410,-p9@USH1C
Hg19::chr11:17555415..17555420,-p11@USH1C
Hg19::chr11:17555421..17555441,-p6@USH1C
Hg19::chr12:131856235..131856282,-p@chr12:131856235..131856282
-
Hg19::chr12:40426483..40426524,-p@chr12:40426483..40426524
-
Hg19::chr12:70944095..70944107,+p@chr12:70944095..70944107
+
Hg19::chr13:46786138..46786153,+p2@LRRC63
Hg19::chr14:88452908..88452916,-p@chr14:88452908..88452916
-
Hg19::chr14:88452922..88452929,-p@chr14:88452922..88452929
-
Hg19::chr14:88452944..88452960,-p@chr14:88452944..88452960
-
Hg19::chr15:22550789..22550806,+p@chr15:22550789..22550806
+
Hg19::chr15:22550810..22550816,+p@chr15:22550810..22550816
+
Hg19::chr15:91143571..91143582,+p@chr15:91143571..91143582
+
Hg19::chr16:3332452..3332454,+p@chr16:3332452..3332454
+
Hg19::chr16:57832004..57832027,-p4@KIFC3
Hg19::chr16:57832028..57832042,-p10@KIFC3
Hg19::chr16:65159735..65159744,-p@chr16:65159735..65159744
-
Hg19::chr16:65159769..65159787,-p@chr16:65159769..65159787
-
Hg19::chr16:65432589..65432593,+p@chr16:65432589..65432593
+
Hg19::chr16:82662683..82662690,-p@chr16:82662683..82662690
-
Hg19::chr17:53809214..53809228,-p5@TMEM100
Hg19::chr17:53809233..53809251,-p3@TMEM100
Hg19::chr17:66511224..66511241,+p29@PRKAR1A
Hg19::chr17:9716257..9716264,-p@chr17:9716257..9716264
-
Hg19::chr17:9739681..9739708,+p5@GLP2R
Hg19::chr17:9739716..9739725,+p13@GLP2R
Hg19::chr17:9739727..9739738,+p11@GLP2R
Hg19::chr18:5478350..5478363,-p10@EPB41L3
Hg19::chr18:5478399..5478403,-p24@EPB41L3
Hg19::chr18:5540365..5540373,-p22@EPB41L3
Hg19::chr18:61368086..61368120,+p@chr18:61368086..61368120
+
Hg19::chr18:61370192..61370197,+p1@SERPINB11
Hg19::chr18:67562993..67563000,-p@chr18:67562993..67563000
-
Hg19::chr18:67563022..67563032,-p@chr18:67563022..67563032
-
Hg19::chr19:46665277..46665280,-p@chr19:46665277..46665280
-
Hg19::chr19:46684088..46684108,-p@chr19:46684088..46684108
-
Hg19::chr19:46684114..46684142,-p@chr19:46684114..46684142
-
Hg19::chr1:154699181..154699196,+p@chr1:154699181..154699196
+
Hg19::chr1:15653306..15653329,+p8@FHAD1
Hg19::chr1:15653374..15653410,+p5@FHAD1
Hg19::chr1:15653436..15653448,+p12@FHAD1
Hg19::chr1:156783663..156783673,-p11@SH2D2A
Hg19::chr1:156785210..156785223,-p10@SH2D2A
Hg19::chr1:156785242..156785247,-p19@SH2D2A
Hg19::chr1:156785292..156785301,-p13@SH2D2A
Hg19::chr1:156786243..156786257,-p6@SH2D2A
Hg19::chr1:188856517..188856523,-p1@ENST00000414765
Hg19::chr1:188856567..188856573,-p2@ENST00000414765
Hg19::chr1:188856590..188856595,-p4@ENST00000414765
Hg19::chr1:188856977..188857009,-p3@ENST00000414765
Hg19::chr1:188857554..188857562,-p@chr1:188857554..188857562
-
Hg19::chr1:188861179..188861222,-p@chr1:188861179..188861222
-
Hg19::chr1:188874798..188874820,+p1@ENST00000445072
Hg19::chr1:234565260..234565271,-p@chr1:234565260..234565271
-
Hg19::chr1:246469346..246469359,-p7@SMYD3
Hg19::chr1:246469406..246469412,-p18@SMYD3
Hg19::chr1:246887738..246887749,+p7@SCCPDH
Hg19::chr1:246887780..246887791,+p6@SCCPDH
Hg19::chr1:54665916..54665927,+p2@MRPL37
Hg19::chr1:68927028..68927036,-p@chr1:68927028..68927036
-
Hg19::chr21:11130568..11130575,+p@chr21:11130568..11130575
+
Hg19::chr2:115929667..115929677,+p@chr2:115929667..115929677
+
Hg19::chr2:228190043..228190054,+p5@MFF
Hg19::chr2:228190066..228190086,+p4@MFF
Hg19::chr3:16739396..16739405,-p5@ENST00000426218
Hg19::chr3:189838995..189839000,-p31@LEPREL1
Hg19::chr3:189839367..189839371,-p16@LEPREL1
Hg19::chr3:189840026..189840048,-p10@LEPREL1
Hg19::chr3:189840061..189840073,-p14@LEPREL1
Hg19::chr3:189840106..189840120,-p18@LEPREL1
Hg19::chr3:63804973..63804980,+p3@C3orf49
Hg19::chr3:63805017..63805035,+p2@C3orf49
Hg19::chr3:63805044..63805054,+p1@C3orf49
Hg19::chr4:103265976..103265993,-p11@SLC39A8
Hg19::chr4:103266043..103266060,-p12@SLC39A8
Hg19::chr4:103266068..103266091,-p10@SLC39A8
Hg19::chr4:103266101..103266106,-p20@SLC39A8
Hg19::chr4:159131359..159131372,+p11@TMEM144
Hg19::chr4:159131486..159131501,+p8@TMEM144
Hg19::chr4:40194268..40194278,+p27@RHOH
Hg19::chr4:74586784..74586789,-p@chr4:74586784..74586789
-
Hg19::chr5:119697827..119697855,+p@chr5:119697827..119697855
+
Hg19::chr5:119697859..119697884,+p@chr5:119697859..119697884
+
Hg19::chr5:136896379..136896398,-p@chr5:136896379..136896398
-
Hg19::chr5:5558678..5558683,+p@chr5:5558678..5558683
+
Hg19::chr5:57878034..57878045,+p9@RAB3C
Hg19::chr5:59744572..59744583,-p57@PDE4D
Hg19::chr5:59783574..59783584,+p6@PART1
Hg19::chr6:1312753..1312800,+p4@FOXQ1
Hg19::chr6:138060034..138060045,-p1@ENST00000411615
p1@ENST00000419220
Hg19::chr6:138060103..138060111,-p3@ENST00000411615
p3@ENST00000419220
Hg19::chr6:138060178..138060193,-p2@ENST00000411615
p2@ENST00000419220
Hg19::chr6:145434485..145434492,+p@chr6:145434485..145434492
+
Hg19::chr6:162477886..162477932,-p@chr6:162477886..162477932
-
Hg19::chr6:166575975..166575983,-p@chr6:166575975..166575983
-
Hg19::chr6:166579326..166579334,-p@chr6:166579326..166579334
-
Hg19::chr6:166581324..166581327,-p7@T
Hg19::chr6:166581333..166581349,-p2@T
Hg19::chr6:166581938..166581955,-p3@T
Hg19::chr6:166582133..166582149,-p1@T
Hg19::chr6:22113567..22113578,+p@chr6:22113567..22113578
+
Hg19::chr6:22113587..22113603,+p@chr6:22113587..22113603
+
Hg19::chr6:22113608..22113630,+p@chr6:22113608..22113630
+
Hg19::chr6:22113639..22113643,+p@chr6:22113639..22113643
+
Hg19::chr6:33644021..33644058,+p@chr6:33644021..33644058
+
Hg19::chr6:36952360..36952367,-p@chr6:36952360..36952367
-
Hg19::chr7:151169194..151169198,-p17@RHEB
Hg19::chr7:158225991..158225999,+p@chr7:158225991..158225999
+
Hg19::chr7:158226043..158226065,+p@chr7:158226043..158226065
+
Hg19::chr7:158237237..158237241,+p@chr7:158237237..158237241
+
Hg19::chr7:158242968..158242975,+p@chr7:158242968..158242975
+
Hg19::chr7:31938679..31938703,-p@chr7:31938679..31938703
-
Hg19::chr7:32083456..32083492,-p@chr7:32083456..32083492
-
Hg19::chr7:68735026..68735050,+p@chr7:68735026..68735050
+
Hg19::chr7:68735078..68735090,+p@chr7:68735078..68735090
+
Hg19::chr7:68735132..68735135,+p@chr7:68735132..68735135
+
Hg19::chr7:68735137..68735150,+p@chr7:68735137..68735150
+
Hg19::chr7:68735214..68735224,+p@chr7:68735214..68735224
+
Hg19::chr8:129431377..129431384,-p@chr8:129431377..129431384
-
Hg19::chr8:52307771..52307797,+p@chr8:52307771..52307797
+
Hg19::chr9:138393091..138393107,+p@chr9:138393091..138393107
+
Hg19::chr9:138393119..138393159,+p@chr9:138393119..138393159
+
Hg19::chr9:138393171..138393178,+p@chr9:138393171..138393178
+
Hg19::chr9:138393188..138393204,+p@chr9:138393188..138393204
+
Hg19::chr9:138393225..138393257,+p@chr9:138393225..138393257
+
Hg19::chr9:138393587..138393606,-p8@C9orf116
Hg19::chr9:138393704..138393727,+p@chr9:138393704..138393727
+
Hg19::chr9:138394283..138394314,+p9@MRPS2
Hg19::chr9:33306373..33306392,+p@chr9:33306373..33306392
+
Hg19::chr9:79009244..79009257,-p4@RFK
Hg19::chrX:110341059..110341099,+p@chrX:110341059..110341099
+
Hg19::chrX:142113711..142113717,+p1@SPANXN4
Hg19::chrX:23803131..23803142,+p7@SAT1


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:0005737cytoplasm0.0191544599457173
GO:0030046parallel actin filament bundle formation0.0435505411641322
GO:0048513organ development0.0435505411641322
GO:0047131saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity0.0435505411641322
GO:0009231riboflavin biosynthetic process0.0435505411641322
GO:0042727riboflavin and derivative biosynthetic process0.0435505411641322
GO:0006771riboflavin metabolic process0.0435505411641322
GO:0004753saccharopine dehydrogenase activity0.0435505411641322
GO:0042726riboflavin and derivative metabolic process0.0435505411641322
GO:0004145diamine N-acetyltransferase activity0.0435505411641322
GO:0001917photoreceptor inner segment0.0435505411641322
GO:0008531riboflavin kinase activity0.0435505411641322
GO:0048598embryonic morphogenesis0.0460967290243841
GO:0044424intracellular part0.0460967290243841
GO:0009887organ morphogenesis0.0460967290243841
GO:0019797procollagen-proline 3-dioxygenase activity0.0460967290243841
GO:0031544peptidyl-proline 3-dioxygenase activity0.0460967290243841



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>

Cell Type
Ontology termp-valuen
epithelial cell of lung6.95e-1219
Uber Anatomy
Ontology termp-valuen
respiratory tract epithelium6.95e-1219
lung epithelium6.95e-1219
lung1.80e-1022
respiratory tube1.80e-1022
respiration organ1.80e-1022
pair of lungs1.80e-1022
lung primordium1.80e-1022
lung bud1.80e-1022
respiratory system epithelium1.52e-0828
thoracic cavity element2.74e-0734
thoracic cavity2.74e-0734
thoracic segment organ4.03e-0735
epithelial bud8.21e-0737
Disease
Ontology termp-valuen
lung large cell carcinoma2.39e-663
non-small cell lung carcinoma1.48e-405
lung carcinoma2.62e-239
lung cancer1.22e-1415
respiratory system cancer8.02e-1416


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)
MA0003.11.10809e-06
MA0004.10.0748804
MA0006.10.218533
MA0007.10.00849506
MA0009.10.443522
MA0014.18.21352e-06
MA0017.10.483058
MA0019.11.26301
MA0024.10.829362
MA0025.11.14856
MA0027.11.32128
MA0028.10.00216479
MA0029.10.890931
MA0030.10.0296339
MA0031.10.0815372
MA0038.10.203626
MA0040.10.316575
MA0041.10.429925
MA0042.10.480908
MA0043.10.774844
MA0046.10.19106
MA0048.10.00204293
MA0050.10.333041
MA0051.10.512774
MA0052.10.137628
MA0055.10.165211
MA0056.10
MA0057.10.00142635
MA0058.10.0410074
MA0059.10.0177954
MA0060.10.034795
MA0061.10.0148528
MA0063.10
MA0066.10.104996
MA0067.10.201274
MA0068.10.0114618
MA0069.10.187628
MA0070.10.400058
MA0071.11.07779
MA0072.11.07501
MA0073.15.29726e-06
MA0074.10.195631
MA0076.10.00913912
MA0077.10.38028
MA0078.10.0355778
MA0081.10.21598
MA0083.10.056911
MA0084.10.326801
MA0087.10.388755
MA0088.10.159825
MA0089.10
MA0090.12.44621
MA0091.10.246411
MA0092.12.12043
MA0093.10.0278308
MA0095.10
MA0098.10
MA0100.10.0501806
MA0101.10.00528814
MA0103.10.125486
MA0105.10.000590721
MA0106.10.065454
MA0107.10.0109837
MA0108.20.649945
MA0109.10
MA0111.10.140776
MA0113.10.168872
MA0114.10.0366618
MA0115.10.157495
MA0116.10.250043
MA0117.10.0668314
MA0119.11.31841
MA0122.10.0761113
MA0124.10.834775
MA0125.10.658903
MA0130.10
MA0131.10.247492
MA0132.10
MA0133.10
MA0135.10.229728
MA0136.10.111487
MA0139.10.00941958
MA0140.10.582593
MA0141.10.314021
MA0142.10.339993
MA0143.10.498068
MA0144.10.0453818
MA0145.10.0226899
MA0146.13.07268e-05
MA0147.10.013297
MA0148.10.299584
MA0149.10.0624766
MA0062.24.71831e-05
MA0035.21.05804
MA0039.24.71534e-06
MA0138.20.104277
MA0002.20.571734
MA0137.20.198293
MA0104.20.00199517
MA0047.20.134787
MA0112.20.0482962
MA0065.20.000141537
MA0150.12.04151
MA0151.10
MA0152.10.417206
MA0153.10.0898046
MA0154.10.00663176
MA0155.10.0105338
MA0156.10.078023
MA0157.10.143449
MA0158.10
MA0159.10.0819765
MA0160.11.21081
MA0161.10
MA0162.11.07731e-05
MA0163.18.94229e-07
MA0164.10.781415
MA0080.20.151508
MA0018.20.941894
MA0099.21.10303
MA0079.20
MA0102.21.66662
MA0258.10.473244
MA0259.10.0578846
MA0442.10



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#1051261.558269460687560.01406092145288990.0493467043791247
NR3C1#2908182.026424210233940.003349432877378720.0172994125058383



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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