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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.601697319106115,0.899834004390776,0.688040251593369,0.928946907498563,1.11620744915815,0.876790188631876,0.665522859598594,0.212645603028643,0.310638626616716,0,0,0.245799139035898,0.433174319314097,0.349794783611619,0.424389409679944,0.223320720221072,0.204850754147253,0,0.172583317114759,0,0,0,0,0,0.0513619522818629,0,0,0,0,0,0.0625128387853364,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.769091936769067,0.52252414898154,0.319283544328196,0.318963865966379,0.43826600016709,0.480637031356009,0.529668719839443,1.06803170426455,0,0,0,0.0534545700183436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.62562246274412,0.289745101127062,0.378285111607663,0.912002957703999,0.383577251490408,0.326613392989952,0.315443408671468,0.298125776038763,0.351186193538355,0.382651330404058,0.378039406110832,0.449677239203374,0.5191325264156,0.0914282698219536,0,0,0.060489586087507,0.0482220752390542,0.0934816315200053,0.0570765567424092,0.0806820944291313,0.0503156775564332,0.15023531915021,0.340047884800798,0.472442344312854,0.281070056064076,0.38689763493088,0.067567801197968,0.0511982733942606,0,0,0.207627795464294,0.342798473351567,0.253828559002334,0.187004028169722,0.35819084011983,0.447067490104915,0.278816063608295,0.209063106658541,0.359494493762296,0.325659543288883,0.284751513701768,0.142936064165064,0.244846235928892,0.376388653791939,0.390018681904133,0.233000982852579,0.0797252919890154,0.068022726550833,0,0,0,0,0,0.0477396614475454,0.0428357178336246,0,0,0,0.466826533052593,0,0.37896153349969,0.23600275090536,0,0,0,0,0,0,0,0,0,0,0,0.540259890483225,0.733218244119286,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0916027365082372,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046155979559586,0.157142363216531,0.0594409392973691,0.458443403529445,0,0.4298500264474,0.284701223916578,0.309645999537164,0,0,0,0.729193319055887,1.14683841087047,0.260843920469556,0.217871311742009,0.721373907919347,0.412276331529905,0.3713731029035,0,0.352010113842064,0,0,0,0.427709039760653,0.647955594616237,0,0.156653296834752,0,0.0715362608323278,0,0,0,0,0,0,0,0,0,0,0,0,0.322352350062305,0.477219985303347,0.188233632538465,0.840506880906517,0.65113032499177,0.483737282391003,0.299908582508999,0.343169104270775,0.515088629055027,0,0,0.13632043160929,0.100594818706322,0.273824123649977,0.592505347576552,0,0,0,0.114986933642873,0.425591991369837,0.424694039532282,0.492263017663224,0.416677638475842,0.781422907798284,0.636460026539023,0.355041839142254,0.700820323277984,0.395183177140817,0.165134204237583,0.3839039749995,0.1739908434077,0.181630511148827,0.334876536979502,0,0,0,0.416208040003401,0.463972616564359,0.375828513209871,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0813768443325499,0,0,0,0,0.62466140623093,0.156610919547238,0.228263261385601,0.300225586849493,0.150298798479565,0.416857379616851,0.501324574162144,0.214485066746331,0.575187048533518,0,0,0,0,0.165791835868262,0.600712871887379,0,0.284227806740343,0,0,0.0738371582016079,0.17586830385699,0.241625348364984,0.21292204628454,0.564526726259544,0.0989542966657617,0.358661294553704,0.213891194797874,0.125812862157168,0.511503752954731,0.880178184214569,0.621100912291672,0.079970395058755,0,0.152673061679609,0.343536453364729,0.346072636530994,0,0.291257682561122,0.809136745252859,0.64248860843547,0.322783652810203,0,0.157895037844406,0.198320387665648,0.472417692728768,0.147929950453612,0.11721277736131,0.107784894264258,0.234784651940436,0.434395546101598,0.132474558164796,0,0.289393926021477,0.473599267420186,0.139713259292333,0.130312767515111,0,0,0,0.0914778548127946,0,0,0,0,0,0,0,0,0,0,0,0,0.0440785955756708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.341181674520914,0.630083098496476,0.315838406393686,0,0,0,0,0,0.174584203487731,0.105947296040957,0,0,0,0.457312177667757,0,0,0,0.078198198554358,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0695293501927681,0,0,0,0,0,0,0,0,0.317499977730368,0.179455868796382,0,0,0,0.214314512399756,0.292530755012065,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.5370783478329,0,0,0,0,1.16565438206995,0,0,0,0,0.0722224018548135,0.665554865164094,0,0.0753862568960672,0,0,0,0,0,0,0,0,0,0,0,0.31140628842589,0,0,0,0,0.0402022792589852,0,0.607365348846892,0,0,0,0,0,0.0840229578243582,0,0,0,0,0,0,0,0.148514003485278,0.197128099808574,0,0.110236269607548,0,0,0,0.26940339545949,0,0.379561486800227,0.0896085685791025,0,0.112496946091474,0,0,0.177103672581591,0.781338709374161,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0329432353726146,0.0827201683234173,0,0,0,0,0,0,0.188365813972295,0.270497510320477,0.296613001671098,0,0,0.706659120706632,0,0,0,0,0,0,0,0.0440642112897698,0.211872352186983,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.529953252159785,0.507607026735872,0.576805268389004,0.195403946339443,0.496349109945355,0.830535287478906,0.19532689222511,0.679280733071713,0.501897013062038,0.24036844179977,0.291320134573091,0.161309027678618,0.319489297861814,0.42468972609494,0.593757647490153,0.523443838004407,0.933875884985973,0.944702147244423,0.302524051762667,0.435533234528474,0.451169002445765,0.165551091449075,0.621671293671031,0.146136648478548,0.662989396331388,0.640232405294876,0,0.076502026345344,0.0843766322300271,0,0.0887404631064488,0,0,0,0.116873766533297,0.297487065114972,0,0,0,0,0,0,0,0,0,0,0.218855645944531,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.356411653548727,0,0,0.467522886342101,0.639282556293514,0,0,0,0,0,0,0,0,0,0,0,0,0.516970451538659,0,0.14545511639796,0.031493427513643,0,0,0,0,0,0,0,0,0,0,0,0.29938140626407,0,0,0,0,0,0,0.209760667568878,0,0,0,0,0,0,0.032817368032432,0,0,0.868768482190127,0,0,0.0299826682885844,0,0.165827456884257,0.229280654886655,0.532134219103551,0,0.0684524727462707,0,0,0,0,0.266413775268255,0,0,0,0,0,0,0,0,1.03514650525955,1.30912758091331,0,0,0.202651883375147,0,0,0,0.0322859259446875,0.517599995525751,0,0.134246905442266,0,0,0,0.548504194982,0.340342926878402,0.0390109377342095,0.0996224845265148,0,0,0,0,0.503928051510997,0,0,0,0,0,0.797127789580883,1.10436701158866,0.69223620720078,0.994161957042363,0,0,0,0,0,0,0,0.0889635065466152,0,0,0,0.0839445661171913,0.636778870489595,0,0.0508240440617333,0,0,0.702632451872836,0.0855462791577618,0.661837409234159,0,0.0300822291072195,0.902322099504744,0,0,0,0,1.29603468539674,0.20715139958257,0.851468880025377,0,0.146917605400546,0
|full_id=C292_Mesenchymal_skin_umbilical_Adipocyte_mesenchymal_Chondrocyte_skeletal
|full_id=C292_Mesenchymal_skin_umbilical_Adipocyte_mesenchymal_Chondrocyte_skeletal
|gostat_on_coexpression_clusters=GO:0005586!collagen type III!0.000853644177557989!1281$GO:0005583!fibrillar collagen!0.00469504297656894!1281$GO:0005581!collagen!0.0153655951960438!1281$GO:0005201!extracellular matrix structural constituent!0.0170728835511598!1281$GO:0044420!extracellular matrix part!0.0170728835511598!1281$GO:0006817!phosphate transport!0.0170728835511598!1281$GO:0003013!circulatory system process!0.0170728835511598!1281$GO:0008015!blood circulation!0.0170728835511598!1281$GO:0015698!inorganic anion transport!0.0246608317961197!1281$GO:0006820!anion transport!0.027572706935123!1281$GO:0009887!organ morphogenesis!0.028092653843272!1281$GO:0005578!proteinaceous extracellular matrix!0.0299486832293261!1281
|gostat_on_coexpression_clusters=GO:0005586!collagen type III!0.000853644177557989!1281$GO:0005583!fibrillar collagen!0.00469504297656894!1281$GO:0005581!collagen!0.0153655951960438!1281$GO:0005201!extracellular matrix structural constituent!0.0170728835511598!1281$GO:0044420!extracellular matrix part!0.0170728835511598!1281$GO:0006817!phosphate transport!0.0170728835511598!1281$GO:0003013!circulatory system process!0.0170728835511598!1281$GO:0008015!blood circulation!0.0170728835511598!1281$GO:0015698!inorganic anion transport!0.0246608317961197!1281$GO:0006820!anion transport!0.027572706935123!1281$GO:0009887!organ morphogenesis!0.028092653843272!1281$GO:0005578!proteinaceous extracellular matrix!0.0299486832293261!1281

Revision as of 15:44, 12 September 2012


Full id: C292_Mesenchymal_skin_umbilical_Adipocyte_mesenchymal_Chondrocyte_skeletal



Phase1 CAGE Peaks

Hg19::chr17:48261721..48261729,-p@chr17:48261721..48261729
-
Hg19::chr2:189839090..189839105,+p1@COL3A1
Hg19::chr2:189849579..189849628,+p@chr2:189849579..189849628
+
Hg19::chr2:189849915..189849949,+p@chr2:189849915..189849949
+
Hg19::chr2:189850401..189850478,+p@chr2:189850401..189850478
+
Hg19::chr2:189851773..189851845,+p4@COL3A1
Hg19::chr2:189852804..189852835,+p@chr2:189852804..189852835
+
Hg19::chr2:189855724..189855761,+p@chr2:189855724..189855761
+
Hg19::chr2:189856903..189856926,+p@chr2:189856903..189856926
+
Hg19::chr2:189857607..189857646,+p@chr2:189857607..189857646
+
Hg19::chr2:189858077..189858096,+p@chr2:189858077..189858096
+
Hg19::chr2:189858136..189858149,+p@chr2:189858136..189858149
+
Hg19::chr2:189858758..189858780,+p@chr2:189858758..189858780
+
Hg19::chr2:189858991..189859033,+p@chr2:189858991..189859033
+
Hg19::chr2:189859261..189859297,+p@chr2:189859261..189859297
+
Hg19::chr2:189859443..189859507,+p@chr2:189859443..189859507
+
Hg19::chr2:189861175..189861198,+p@chr2:189861175..189861198
+
Hg19::chr2:189864003..189864023,+p@chr2:189864003..189864023
+
Hg19::chr2:189864188..189864235,+p@chr2:189864188..189864235
+
Hg19::chr2:189864267..189864279,+p@chr2:189864267..189864279
+
Hg19::chr2:189866256..189866277,+p@chr2:189866256..189866277
+
Hg19::chr2:189867024..189867049,+p@chr2:189867024..189867049
+
Hg19::chr2:189869053..189869071,+p19@COL3A1
Hg19::chr2:189873664..189873737,+p2@COL3A1
Hg19::chr2:189873740..189873791,+p3@COL3A1
Hg19::chr2:189873796..189873815,+p12@COL3A1
Hg19::chr2:189873877..189873903,+p10@COL3A1
Hg19::chr2:189874898..189874924,+p@chr2:189874898..189874924
+
Hg19::chr2:189874955..189875006,+p@chr2:189874955..189875006
+
Hg19::chr2:189875363..189875390,+p@chr2:189875363..189875390
+
Hg19::chr2:189875404..189875442,+p@chr2:189875404..189875442
+
Hg19::chr2:189875563..189875584,+p@chr2:189875563..189875584
+
Hg19::chr2:189876360..189876377,+p4@AF130082
Hg19::chr2:189876383..189876417,+p3@AF130082
Hg19::chr2:189876466..189876506,+p1@AF130082
Hg19::chr2:189876532..189876594,+p2@AF130082
Hg19::chr2:189876664..189876675,+p10@AF130082
Hg19::chr2:189876710..189876721,+p7@AF130082
Hg19::chr2:189876741..189876752,+p9@AF130082
Hg19::chr2:189876820..189876830,+p11@AF130082
Hg19::chr2:189876888..189876899,+p12@AF130082
Hg19::chr2:189877182..189877191,+p@chr2:189877182..189877191
+
Hg19::chr2:189877298..189877309,+p@chr2:189877298..189877309
+
Hg19::chr2:189877348..189877367,+p@chr2:189877348..189877367
+


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:0005586collagen type III0.000853644177557989
GO:0005583fibrillar collagen0.00469504297656894
GO:0005581collagen0.0153655951960438
GO:0005201extracellular matrix structural constituent0.0170728835511598
GO:0044420extracellular matrix part0.0170728835511598
GO:0006817phosphate transport0.0170728835511598
GO:0003013circulatory system process0.0170728835511598
GO:0008015blood circulation0.0170728835511598
GO:0015698inorganic anion transport0.0246608317961197
GO:0006820anion transport0.027572706935123
GO:0009887organ morphogenesis0.028092653843272
GO:0005578proteinaceous extracellular matrix0.0299486832293261



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>

Uber Anatomy
Ontology termp-valuen
somite2.65e-1983
paraxial mesoderm2.65e-1983
presomitic mesoderm2.65e-1983
presumptive segmental plate2.65e-1983
trunk paraxial mesoderm2.65e-1983
presumptive paraxial mesoderm2.65e-1983
dermomyotome3.51e-1870
muscle tissue1.45e-1763
musculature1.45e-1763
musculature of body1.45e-1763
skeletal muscle tissue2.16e-1761
striated muscle tissue2.16e-1761
myotome2.16e-1761
trunk mesenchyme6.66e-16143
multilaminar epithelium1.59e-1382
multi-tissue structure1.98e-12347
multi-cellular organism1.44e-11659
organism subdivision4.13e-11365
trunk4.40e-11216
mesenchyme4.57e-11238
entire embryonic mesenchyme4.57e-11238
splanchnic layer of lateral plate mesoderm4.24e-1084
primary circulatory organ3.86e-0827
heart3.96e-0824
primitive heart tube3.96e-0824
primary heart field3.96e-0824
anterior lateral plate mesoderm3.96e-0824
heart tube3.96e-0824
heart primordium3.96e-0824
cardiac mesoderm3.96e-0824
cardiogenic plate3.96e-0824
heart rudiment3.96e-0824
unilaminar epithelium1.71e-07138
adipose tissue3.44e-0714
extraembryonic structure4.12e-0724
organ component layer4.96e-0757
tissue7.91e-07787
mesoderm8.49e-07448
mesoderm-derived structure8.49e-07448
presumptive mesoderm8.49e-07448


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

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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