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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:39, 17 September 2013


Full id: C134_skeletal_diaphragm_tongue_throat_Skeletal_skin_penis



Phase1 CAGE Peaks

Hg19::chr10:75391836..75391847,-p@chr10:75391836..75391847
-
Hg19::chr11:111783450..111783475,+p1@C11orf52
p1@HSPB2-C11orf52
p1@HSPB2
Hg19::chr11:111783485..111783497,+p2@HSPB2-C11orf52
Hg19::chr11:111783512..111783526,+p3@HSPB2-C11orf52
Hg19::chr11:1942566..1942578,+p14@TNNT3
Hg19::chr11:1942580..1942639,+p2@TNNT3
Hg19::chr11:1942642..1942649,+p13@TNNT3
Hg19::chr11:19835258..19835277,+p@chr11:19835258..19835277
+
Hg19::chr11:2170786..2170809,-p66@IGF2
Hg19::chr11:47206965..47206974,-p9@PACSIN3
Hg19::chr11:66633918..66633936,-p@chr11:66633918..66633936
-
Hg19::chr11:9450312..9450317,+p1@SNORA23
Hg19::chr12:3068942..3068953,+p13@TEAD4
Hg19::chr12:56548579..56548595,+p@chr12:56548579..56548595
+
Hg19::chr12:57112913..57112922,-p@chr12:57112913..57112922
-
Hg19::chr12:57114812..57114823,-p@chr12:57114812..57114823
-
Hg19::chr12:57115086..57115092,-p@chr12:57115086..57115092
-
Hg19::chr14:101356593..101356602,-p@chr14:101356593..101356602
-
Hg19::chr14:24600866..24600882,+p2@FITM1
Hg19::chr14:24601686..24601718,+p6@FITM1
Hg19::chr14:81916474..81916483,-p3@ENST00000555001
Hg19::chr14:81916503..81916517,-p1@ENST00000555001
Hg19::chr14:94423318..94423330,-p12@ASB2
Hg19::chr15:42651691..42651715,+p2@CAPN3
Hg19::chr15:77089901..77089941,-p@chr15:77089901..77089941
-
Hg19::chr16:30383613..30383616,+p@chr16:30383613..30383616
+
Hg19::chr16:30384030..30384072,+p@chr16:30384030..30384072
+
Hg19::chr16:30387474..30387490,+p@chr16:30387474..30387490
+
Hg19::chr16:30389152..30389161,+p23@ZNF48
Hg19::chr16:47430125..47430142,-p9@ITFG1
Hg19::chr16:67426950..67426958,-p@chr16:67426950..67426958
-
Hg19::chr16:67427030..67427043,-p@chr16:67427030..67427043
-
Hg19::chr16:89238149..89238187,+p1@CDH15
Hg19::chr16:89238188..89238199,+p3@CDH15
Hg19::chr16:89238212..89238224,+p2@CDH15
Hg19::chr17:10299730..10299770,-p@chr17:10299730..10299770
-
Hg19::chr17:10299918..10299924,-p@chr17:10299918..10299924
-
Hg19::chr17:10303744..10303773,+p@chr17:10303744..10303773
+
Hg19::chr17:10310119..10310123,-p@chr17:10310119..10310123
-
Hg19::chr17:10323360..10323378,+p@chr17:10323360..10323378
+
Hg19::chr17:10323363..10323366,-p3@MYH8
Hg19::chr17:10325261..10325267,-p1@MYH8
Hg19::chr17:10325303..10325311,-p2@MYH8
Hg19::chr17:10533450..10533457,+p@chr17:10533450..10533457
+
Hg19::chr17:10537375..10537387,-p@chr17:10537375..10537387
-
Hg19::chr17:10537430..10537439,-p@chr17:10537430..10537439
-
Hg19::chr17:10537442..10537452,-p@chr17:10537442..10537452
-
Hg19::chr17:10539045..10539068,+p@chr17:10539045..10539068
+
Hg19::chr17:10541616..10541630,-p@chr17:10541616..10541630
-
Hg19::chr17:10541701..10541714,+p@chr17:10541701..10541714
+
Hg19::chr17:10542429..10542477,+p@chr17:10542429..10542477
+
Hg19::chr17:10542690..10542702,-p2@MYH3
Hg19::chr17:10542721..10542730,-p6@MYH3
Hg19::chr17:10542947..10542952,+p@chr17:10542947..10542952
+
Hg19::chr17:10543000..10543023,+p@chr17:10543000..10543023
+
Hg19::chr17:10543362..10543373,-p8@MYH3
Hg19::chr17:10543535..10543570,-p3@MYH3
Hg19::chr17:10544511..10544520,-p@chr17:10544511..10544520
-
Hg19::chr17:10555831..10555857,-p@chr17:10555831..10555857
-
Hg19::chr17:10560619..10560631,-p1@MYH3
Hg19::chr17:10560665..10560669,-p5@MYH3
Hg19::chr17:25904469..25904479,+p12@KSR1
Hg19::chr17:40563207..40563209,-p@chr17:40563207..40563209
-
Hg19::chr17:45286297..45286312,+p5@MYL4
Hg19::chr17:65040577..65040582,+p4@CACNG1
Hg19::chr17:65040646..65040675,+p2@CACNG1
Hg19::chr17:65040678..65040733,+p1@CACNG1
Hg19::chr17:65040737..65040746,+p3@CACNG1
Hg19::chr17:65040748..65040753,+p5@CACNG1
Hg19::chr18:3193857..3193869,+p@chr18:3193857..3193869
+
Hg19::chr18:3220187..3220208,-p6@MYOM1
Hg19::chr18:55922928..55922935,+p@chr18:55922928..55922935
+
Hg19::chr19:14217762..14217764,-p@chr19:14217762..14217764
-
Hg19::chr19:14228521..14228536,-p2@PRKACA
Hg19::chr19:18554708..18554716,-p3@ENST00000541164
Hg19::chr19:18554726..18554736,-p2@ENST00000541164
Hg19::chr19:18554761..18554768,-p4@ENST00000541164
Hg19::chr19:33977922..33977934,-p@chr19:33977922..33977934
-
Hg19::chr19:34884793..34884811,+p@chr19:34884793..34884811
+
Hg19::chr19:34884817..34884868,+p@chr19:34884817..34884868
+
Hg19::chr19:46843663..46843674,+p8@HIF3A
Hg19::chr19:48283801..48283815,+p@chr19:48283801..48283815
+
Hg19::chr19:49222956..49222990,-p2@MAMSTR
Hg19::chr19:57417488..57417493,+p@chr19:57417488..57417493
+
Hg19::chr1:1846519..1846531,+p5@CALML6
Hg19::chr1:1846693..1846705,+p4@CALML6
Hg19::chr1:204420155..204420164,-p@chr1:204420155..204420164
-
Hg19::chr1:229567498..229567506,-p@chr1:229567498..229567506
-
Hg19::chr1:229568499..229568505,+p@chr1:229568499..229568505
+
Hg19::chr1:23743877..23743887,-p@chr1:23743877..23743887
-
Hg19::chr1:26316072..26316085,-p@chr1:26316072..26316085
-
Hg19::chr1:6615362..6615371,+p3@TAS1R1
Hg19::chr1:9129895..9129902,-p19@SLC2A5
Hg19::chr20:36152838..36152861,-p4@BLCAP
Hg19::chr20:36152878..36152889,-p9@BLCAP
Hg19::chr20:55091871..55091878,+p3@FAM209A
Hg19::chr20:57427765..57427783,+p51@GNAS
Hg19::chr22:36246064..36246069,-p@chr22:36246064..36246069
-
Hg19::chr22:36246136..36246155,-p@chr22:36246136..36246155
-
Hg19::chr22:36246158..36246175,-p@chr22:36246158..36246175
-
Hg19::chr2:127861232..127861245,-p@chr2:127861232..127861245
-
Hg19::chr2:179659754..179659767,+p@chr2:179659754..179659767
+
Hg19::chr2:220360850..220360855,+p@chr2:220360850..220360855
+
Hg19::chr2:233390904..233390920,+p2@CHRND
Hg19::chr2:233404417..233404428,+p3@CHRNG
Hg19::chr2:233404429..233404447,+p1@CHRNG
Hg19::chr2:24714729..24714761,+p1@NCOA1
Hg19::chr2:71681010..71681037,+p7@DYSF
Hg19::chr3:130236014..130236030,+p@chr3:130236014..130236030
+
Hg19::chr3:52869205..52869238,-p2@MUSTN1
Hg19::chr3:8775466..8775512,+p1@CAV3
Hg19::chr4:172396418..172396419,+p@chr4:172396418..172396419
+
Hg19::chr4:34898792..34898800,+p@chr4:34898792..34898800
+
Hg19::chr4:671754..671765,+p8@MYL5
Hg19::chr4:671780..671793,+p5@MYL5
Hg19::chr5:138730459..138730471,-p@chr5:138730459..138730471
-
Hg19::chr5:148758849..148758861,-p1@IL17B
Hg19::chr6:12007918..12007931,+p1@ENST00000437559
Hg19::chr6:12007963..12007974,+p3@ENST00000437559
Hg19::chr6:150621376..150621399,+p@chr6:150621376..150621399
+
Hg19::chr6:41020934..41020948,+p1@APOBEC2
Hg19::chr6:52001069..52001073,+p@chr6:52001069..52001073
+
Hg19::chr8:144523662..144523672,-p@chr8:144523662..144523672
-
Hg19::chr9:118024813..118024828,-p@chr9:118024813..118024828
-
Hg19::chr9:35683115..35683137,-p@chr9:35683115..35683137
-
Hg19::chr9:35684272..35684277,-p@chr9:35684272..35684277
-
Hg19::chr9:97356126..97356142,-p3@FBP2
Hg19::chrX:105445717..105445733,+p4@MUM1L1
Hg19::chrX:110513769..110513778,-p5@CAPN6
Hg19::chrX:119495934..119495950,+p1@ATP1B4
Hg19::chrX:125953692..125953697,+p3@CXorf64
Hg19::chrX:125953702..125953722,+p1@CXorf64
Hg19::chrX:130192273..130192296,+p2@ARHGAP36
Hg19::chrX:130192318..130192323,+p1@ARHGAP36
Hg19::chrX:63450480..63450511,-p2@ASB12
Hg19::chrX:99839925..99839938,+p1@TNMD


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
0.0006227450480061330.02627984102585883116Vascular smooth muscle contraction (KEGG):04270
0.0009259906422873520.03447953391575853133Tight junction (KEGG):04530
5.78723999284568e-050.0052333184506733352Taste transduction (KEGG):04742
0.001030126349370380.03622610995285833138Insulin signaling pathway (KEGG):04910
0.0004156107932587890.01879154515234383101GnRH signaling pathway (KEGG):04912
0.0004156107932587890.01879154515234383101Melanogenesis (KEGG):04916
4.83907462305162e-050.00510522372731946349Endocrine and other factor-regulated calcium reabsorption (KEGG):04961
8.18467518057476e-060.00103617987786076489Salivary secretion (KEGG):04970
3.91749345114846e-060.000619943338644243474Gastric acid secretion (KEGG):04971
0.0001468618346024030.0103292823670356371Bile secretion (KEGG):04976
0.0002962104988726520.0187501245786389390Dilated cardiomyopathy (KEGG):05414
0.0004156107932587890.01879154515234383101Integrin-mediated cell adhesion (Wikipathways):WP185
0.001438674903055320.04793059019126423155Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
2.63651271987377e-091.6689125516801e-06539Striated Muscle Contraction (Wikipathways):WP383
0.0003761868753793850.0187915451523438220Estrogen signaling pathway (Wikipathways):WP712
0.0007918330870943840.03132689650817163126Metabolism of carbohydrates (Reactome):REACT_474
7.4030763311946e-070.000234307365882309449Muscle contraction (Reactome):REACT_17044
3.34548286755118e-060.0006199433386442436288{ACTB,297} (Static Module):NA
6.84953780566463e-050.00541969678873214355{HTT,61} (Static Module):NA



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:0003012muscle system process1.63605652331798e-11
GO:0006936muscle contraction1.63605652331798e-11
GO:0044449contractile fiber part3.97892675944685e-09
GO:0005859muscle myosin complex3.97892675944685e-09
GO:0043292contractile fiber3.97892675944685e-09
GO:0016460myosin II complex3.97892675944685e-09
GO:0006941striated muscle contraction3.71982413382398e-06
GO:0016459myosin complex4.5435415326943e-06
GO:0008307structural constituent of muscle4.88538578350844e-06
GO:0030017sarcomere7.61010017952327e-06
GO:0030016myofibril1.0373423694782e-05
GO:0015629actin cytoskeleton1.69922111733134e-05
GO:0032982myosin filament1.69922111733134e-05
GO:0005863striated muscle thick filament1.69922111733134e-05
GO:0007517muscle development2.57050151792898e-05
GO:0032501multicellular organismal process5.4432279681343e-05
GO:0003008system process5.78157480686019e-05
GO:0043234protein complex0.00234438634079895
GO:0042383sarcolemma0.00276217692501124
GO:0015464acetylcholine receptor activity0.00457728242701335
GO:0042166acetylcholine binding0.00479214619601587
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.00500673024976491
GO:0044430cytoskeletal part0.00591913125683937
GO:0004198calcium-dependent cysteine-type endopeptidase activity0.00785538890721668
GO:0042391regulation of membrane potential0.00805604221009237
GO:0006937regulation of muscle contraction0.012280248506066
GO:0043176amine binding0.0142242377973511
GO:0048513organ development0.0142242377973511
GO:0015755fructose transport0.0142242377973511
GO:0031852mu-type opioid receptor binding0.0142242377973511
GO:0031628opioid receptor binding0.0142242377973511
GO:0005886plasma membrane0.0150953330950706
GO:0032991macromolecular complex0.0169128604294968
GO:0042132fructose-bisphosphatase activity0.0244850393232612
GO:0050917sensory perception of umami taste0.0244850393232612
GO:0043409negative regulation of MAPKKK cascade0.0244850393232612
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0291384206340225
GO:0005856cytoskeleton0.0322324526947415
GO:0005353fructose transmembrane transporter activity0.0322324526947415
GO:0016556mRNA modification0.0322324526947415
GO:0051925regulation of calcium ion transport via voltage-gated calcium channel0.0322324526947415
GO:0008092cytoskeletal protein binding0.0338960784748465
GO:0005509calcium ion binding0.0342939600311016
GO:0051354negative regulation of oxidoreductase activity0.037471473076189
GO:0031579lipid raft organization and biogenesis0.037471473076189
GO:0045806negative regulation of endocytosis0.037471473076189
GO:0051001negative regulation of nitric-oxide synthase activity0.037471473076189
GO:0046716muscle maintenance0.0449050584866388
GO:0030315T-tubule0.0449050584866388
GO:0048731system development0.0471115443514867
GO:0051049regulation of transport0.0479835796689636
GO:0005861troponin complex0.0479835796689636
GO:0031594neuromuscular junction0.0479835796689636
GO:0006349genetic imprinting0.0479835796689636
GO:0004126cytidine deaminase activity0.0479835796689636



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
cell of skeletal muscle1.34e-189


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)
MA0003.10.43945
MA0004.10.131251
MA0006.10.130037
MA0007.10.293649
MA0009.10.0518522
MA0014.10.0548845
MA0017.10.324703
MA0019.10.143507
MA0024.10.0262684
MA0025.10.100524
MA0027.11.31183
MA0028.10.00563967
MA0029.10.0301716
MA0030.10.0278135
MA0031.10.0167869
MA0038.10.0115376
MA0040.10.128204
MA0041.10.00331094
MA0042.10.00814365
MA0043.10.193007
MA0046.10.0486804
MA0048.15.56615
MA0050.10.197578
MA0051.10.0930732
MA0052.11.7361
MA0055.18.41642
MA0056.10
MA0057.10.483454
MA0058.10.036283
MA0059.10.0355023
MA0060.10.000187201
MA0061.10.744555
MA0063.10
MA0066.11.59321
MA0067.10.195646
MA0068.10.381854
MA0069.10.17973
MA0070.10.170176
MA0071.11.03057
MA0072.10.166414
MA0073.12.80572
MA0074.10.945093
MA0076.10.000435568
MA0077.10.160064
MA0078.10.370159
MA0081.10.197845
MA0083.10.19952
MA0084.10.319902
MA0087.10.164385
MA0088.11.15362
MA0089.10
MA0090.11.43636
MA0091.15.08962
MA0092.10.155419
MA0093.10.0473436
MA0095.10
MA0098.10
MA0100.10.212846
MA0101.10.0503278
MA0103.11.37679
MA0105.10.505058
MA0106.10.0605145
MA0107.10.0610484
MA0108.20.932244
MA0109.10
MA0111.10.820375
MA0113.10.158388
MA0114.11.0789
MA0115.10.152495
MA0116.10.309447
MA0117.10.849753
MA0119.11.49806
MA0122.10.540689
MA0124.10.131179
MA0125.10.64058
MA0130.10
MA0131.10.111181
MA0132.10
MA0133.10
MA0135.10.220918
MA0136.10.0428787
MA0139.10.024558
MA0140.10.0635903
MA0141.11.93661
MA0142.10.0126668
MA0143.10.292601
MA0144.10.0109363
MA0145.11.31762
MA0146.10.292008
MA0147.10.0111136
MA0148.11.06066
MA0149.10.0215026
MA0062.28.00016e-06
MA0035.20.0630987
MA0039.21.26519
MA0138.22.33843
MA0002.20.775442
MA0137.20.114243
MA0104.20.00808322
MA0047.20.841644
MA0112.26.96254
MA0065.21.86685
MA0150.10.264232
MA0151.10
MA0152.10.140535
MA0153.10.0861155
MA0154.11.28263
MA0155.14.57488
MA0156.17.77944e-06
MA0157.10.0489786
MA0158.10
MA0159.13.02958
MA0160.10.049956
MA0161.10
MA0162.10.000765507
MA0163.15.44773
MA0164.10.509169
MA0080.20.0107779
MA0018.20.140634
MA0099.20.394507
MA0079.22.1985
MA0102.20.34724
MA0258.11.35739
MA0259.10.366845
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

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

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