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Coexpression cluster:C309: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.17e-22!115;UBERON:0001049!1.04e-18!57;UBERON:0005068!1.04e-18!57;UBERON:0006241!1.04e-18!57;UBERON:0007135!1.04e-18!57;UBERON:0005743!3.94e-18!86;UBERON:0000073!4.55e-18!94;UBERON:0001016!4.55e-18!94;UBERON:0001017!2.49e-17!82;UBERON:0002346!3.24e-16!90;UBERON:0002780!9.54e-16!41;UBERON:0001890!9.54e-16!41;UBERON:0006240!9.54e-16!41;UBERON:0003075!1.97e-15!86;UBERON:0007284!1.97e-15!86;UBERON:0002616!2.24e-15!59;UBERON:0000924!4.10e-15!173;UBERON:0006601!4.10e-15!173;UBERON:0003080!6.00e-15!42;UBERON:0000153!7.51e-15!129;UBERON:0007811!7.51e-15!129;UBERON:0000033!1.07e-14!123;UBERON:0004121!2.32e-14!169;UBERON:0002020!5.88e-13!34;UBERON:0003528!5.88e-13!34;UBERON:0001893!1.40e-12!34;UBERON:0001869!1.45e-12!32;UBERON:0000955!1.80e-12!69;UBERON:0006238!1.80e-12!69;UBERON:0000475!2.69e-12!365;UBERON:0002791!2.92e-12!33;UBERON:0003056!9.74e-12!61;UBERON:0000468!1.48e-10!659;UBERON:0000956!1.21e-08!25;UBERON:0000203!1.21e-08!25;UBERON:0002619!1.35e-08!22;UBERON:0000481!2.43e-08!347;UBERON:0001950!4.39e-08!20;UBERON:0000480!2.85e-07!626;UBERON:0000467!3.72e-07!625;UBERON:0003102!4.74e-07!95;UBERON:0000477!5.48e-07!286;UBERON:0000914!6.68e-07!83;UBERON:0002329!6.68e-07!83;UBERON:0003077!6.68e-07!83;UBERON:0003059!6.68e-07!83;UBERON:0007282!6.68e-07!83;UBERON:0009618!6.68e-07!83;UBERON:0007285!6.68e-07!83
|ontology_enrichment_uberon=UBERON:0007023!1.17e-22!115;UBERON:0001049!1.04e-18!57;UBERON:0005068!1.04e-18!57;UBERON:0006241!1.04e-18!57;UBERON:0007135!1.04e-18!57;UBERON:0005743!3.94e-18!86;UBERON:0000073!4.55e-18!94;UBERON:0001016!4.55e-18!94;UBERON:0001017!2.49e-17!82;UBERON:0002346!3.24e-16!90;UBERON:0002780!9.54e-16!41;UBERON:0001890!9.54e-16!41;UBERON:0006240!9.54e-16!41;UBERON:0003075!1.97e-15!86;UBERON:0007284!1.97e-15!86;UBERON:0002616!2.24e-15!59;UBERON:0000924!4.10e-15!173;UBERON:0006601!4.10e-15!173;UBERON:0003080!6.00e-15!42;UBERON:0000153!7.51e-15!129;UBERON:0007811!7.51e-15!129;UBERON:0000033!1.07e-14!123;UBERON:0004121!2.32e-14!169;UBERON:0002020!5.88e-13!34;UBERON:0003528!5.88e-13!34;UBERON:0001893!1.40e-12!34;UBERON:0001869!1.45e-12!32;UBERON:0000955!1.80e-12!69;UBERON:0006238!1.80e-12!69;UBERON:0000475!2.69e-12!365;UBERON:0002791!2.92e-12!33;UBERON:0003056!9.74e-12!61;UBERON:0000468!1.48e-10!659;UBERON:0000956!1.21e-08!25;UBERON:0000203!1.21e-08!25;UBERON:0002619!1.35e-08!22;UBERON:0000481!2.43e-08!347;UBERON:0001950!4.39e-08!20;UBERON:0000480!2.85e-07!626;UBERON:0000467!3.72e-07!625;UBERON:0003102!4.74e-07!95;UBERON:0000477!5.48e-07!286;UBERON:0000914!6.68e-07!83;UBERON:0002329!6.68e-07!83;UBERON:0003077!6.68e-07!83;UBERON:0003059!6.68e-07!83;UBERON:0007282!6.68e-07!83;UBERON:0009618!6.68e-07!83;UBERON:0007285!6.68e-07!83
|tfbs_overrepresentation=0.00136264,1.8937e-13,0.982422,0.470376,2.29342e-06,0.642702,0.435308,0.0259651,1.66912e-12,0.287192,0.0148921,0.963838,1.96008e-12,0.826303,0.348359,0.56425,4.82844e-15,0.739131,9.3537e-17,0.773858,0.933959,0.842602,0.671075,0.0105404,2.11293e-18,1.31147e-16,1.63312e-11,7.51485e-07,0.328049,0.720364,0.572675,0.792821,0.210651,3.83379e-25,0.000333482,0.318251,0.997483,0.435008,0.811191,0.592385,1.72038e-08,0.276716,0.00408577,0.492495,0.812764,0.381148,0.395803,8.95108e-22,0.00495065,0.500389,0.639334,9.8773e-07,0.244286,0.718858,0.000208465,0.0930237,0.0175514,0.816558,0.653646,0.000135319,0.0584516,0.000341732,0.0183198,3.24955e-50,4.00247e-10,0.49008,2.13783e-06,0.552689,0.689649,0.424065,0.173192,0.0646806,0.70248,0.00702356,0.0929464,0.20105,0.0112961,0.440556,0.38951,0.0902872,0.729288,0.0212394,0.000299606,0.795241,0.988629,0.726502,0.578761,5.06047e-24,0.993413,0.206533,0.688253,0.142427,0.0434114,0.4679,0.32299,1.51635e-08,0.999865,2.26324e-11,3.33356e-25,0.0615701,0.536827,0.00138063,0.863175,0.0137162,0.00588056,0.103597,0.593997,4.68659e-05,0.867953,2.4869e-05,0.927279,0.362149,5.47191e-08,0.207029,0.75026,0.360046,0.234425,3.74776e-11,0.857143,0.00625354,0.9066,0.956808,0.859502,0.688368,0.754372,0.464113,0.709416,0.176137,3.80842e-07,0.848068,0.190682,0.636209,1.57572e-05,0.25892,0.521418,0.774001,0.581814,0.522903,0.00107201,0.0502156,3.31337e-14,0.529588,0.948428,3.89509e-14,0.297589,1.84444e-12,2.23718e-10,0.681405,4.66051e-13,0.812531,0.945599,0.0541445,0.01689,0.295481,5.69827e-10,2.45032e-10,0.635824,2.11813e-12,0.498462,0.35981,0.96524,0.373789,0.00139474,6.38239e-05,0.984288,0.793542,0.412055,0.528524,0.000235517,5.15401e-08,5.92531e-07,0.573695,0.999698,0.514961,0.294744,7.87579e-09,0.859949,0.123809,0.922331,0.376057,0.894465,0.242362,0.303197,0.797418,0.262619,0.806951,9.51328e-05,0.100392,0.675209,0.916105,6.6135e-10,0.932529,0.818276,0.655939,0.0212335,0.465713,9.58078e-12,0.0486284,0.597719,0.779127,0.703607,0.555091,0.334438,0.556355,8.39587e-07,0.0023671,9.18959e-08,9.4386e-09,1.45314e-28,0.92222,0.00356732,0.761354,1.07683e-05,0.00114662,0.0600871,2.0376e-13,0.902878,0.749252,0.0542424,0.756575,1.29606e-06,0.722517,0.378831,0.89797,0.631195,0.827933,0.856778,0.68921,0.55543,0.551991,0.994946,0.000106808,0.42629,0.021186,0.730421,0.719661,0.466835,2.94412e-14,0.901815,1.18714e-09,7.21872e-07,0.996228,0.739872,0.10523,0.0797867,0.000828504,2.75829e-07,2.84255e-75,6.4984e-05,0.801704,4.83515e-18,1.85613e-20,0.930833,0.73848,0.738711,0.39374,0.771156,0.946662,0.608431,0.350372,0.56438,0.918113,5.22589e-35,5.65065e-08,0.366565,0.666815,0.0996679,0.0387911,0.804749,0.000660536,0.924555,0.00183454,8.7835e-10,0.64804,0.691927,0.396042,0.836837,6.13941e-05,0.277641,0.769701,0.999972,3.33842e-16,0.999961,0.904012,0.0445966,1.48274e-14,0.980584,0.880841,0.997718,0.707192,0.000799684,0.00751898,0.958562,0.965735,0.000653503,0.964103,9.20793e-26,0.825505,3.92944e-30,0.642786,5.90026e-28,5.71926e-16,1.78333e-07,4.22431e-05,6.02378e-38,0.000477062,0.780139,1.6459e-07,0.829083,0.0649396,1.54e-07,0.0187864,0.0944009,8.51495e-05,1.59314e-19,2.65863e-08,1.97589e-23,0.629028,0.526908,5.18147e-07,0.326353,9.02538e-09,0.231141,2.89974e-28,0.980154,1.27867e-06,0.148773,0.722631,0.999986,0.0167185,0.000432712,0.102195,0.970593,0.46873,0.997923,0.140119,0.407592,6.57644e-06,2.13687e-11,0.927014,0.00386784,0.475835,0.522963,0.984806,3.69681e-08,0.132649,0.0260232,4.48735e-05,4.85532e-33,6.27867e-07,0.00270086,0.995397,0.00476056,0.00499359,1.27442e-09,6.34262e-08,0.0857388,4.40806e-05,0.627207,1.91729e-19,0.831657,0.596109,0.0408761,0.999014,0.0231776,1.05534e-05,6.00426e-49,0.999559,0.959525,1.45755e-05,0.379062,0.451209,0.635791,0.000212385,0.392979,0.889926,0.999885,0.47522,0.465429,5.94512e-21,0.161065,0.149524,0.426044,0.794387,0.478558,0.00797527,0.0554254,5.42505e-08,2.60728e-10,0.182542,0.916958,0.181282,0.00325624,0.0296025,0.000801803,1,0.00121411,0.60301,0.00509591,0.302661,0.732587,0.366878,3.28278e-11,0.00184752,2.88594e-06,0.462043,0.852938,0.0185581,2.13872e-14,0.000501971,7.10845e-05,0.989114,0.987141,0.972879,1.06338e-11,0.33931,0.84223,0.0238642,0.0100358,0.931195,1.51485e-20,2.49461e-37,1.75108e-08,8.52832e-05,0.828458,0.239238,0.425345,0.999929,7.19127e-05,0.000466061,1.91072e-11,7.16276e-09,4.27195e-21,0.995426,0.99257,0.0315536,0.140592,0.532947,0.361474,3.99275e-68,3.7152e-11,6.98841e-09,4.87872e-09,0.934884,0.00810893,0.00901565,0.0677461,0.0969061,0.00476158,2.9398e-07,0.00197421,0.00258903,8.87735e-12,0.0178121,0.998894,0.870269,0.609443,0.525181,0.937979,1.73385e-08,0.53735,6.30024e-17,5.29447e-20,0.948202,0.0238614,0.144542,0.937208,4.25598e-32,2.5168e-42,0.43937,1.28617e-16,0.00048196,1.92708e-15,3.97922e-14,0.984245,0.569607,0.998057,0.209385,0.948589,0.423147,0.0317623,0.461394,0.910728,0.794449,0.762053,0.706353,5.08762e-09,0.896063,0.433032,0.441843,0.0494136,0.246745,0.036248,0.0911884,1.80302e-10,0.10802,0.486491,0.310092,0.592334,1.94369e-05,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}}
}}

Revision as of 18:53, 8 August 2012


Full id: C309_normal_Chondrocyte_small_Fibroblast_tenocyte_neuroepithelioma_Osteoblast



Phase1 CAGE Peaks

Hg19::chr10:15760985..15760992,-p@chr10:15760985..15760992
-
Hg19::chr11:68105668..68105675,-p@chr11:68105668..68105675
-
Hg19::chr14:61119131..61119168,+p@chr14:61119131..61119168
+
Hg19::chr14:61125184..61125196,-p8@SIX1
Hg19::chr17:54893192..54893195,-p14@C17orf67
Hg19::chr17:54893196..54893207,-p9@C17orf67
Hg19::chr17:54893213..54893220,-p12@C17orf67
Hg19::chr17:54893269..54893278,-p11@C17orf67
Hg19::chr17:54893292..54893300,-p13@C17orf67
Hg19::chr8:57353655..57353662,-p@chr8:57353655..57353662
-
Hg19::chr8:57353666..57353675,-p@chr8:57353666..57353675
-
Hg19::chr8:57353745..57353754,-p@chr8:57353745..57353754
-
Hg19::chr8:57353804..57353821,-p@chr8:57353804..57353821
-
Hg19::chr8:57353888..57353898,-p@chr8:57353888..57353898
-
Hg19::chr8:57353982..57353991,-p@chr8:57353982..57353991
-
Hg19::chr8:57353995..57354004,-p@chr8:57353995..57354004
-
Hg19::chr8:57354052..57354105,+p@chr8:57354052..57354105
+
Hg19::chr8:57354119..57354137,+p@chr8:57354119..57354137
+
Hg19::chr8:57354124..57354145,-p@chr8:57354124..57354145
-
Hg19::chr8:57354143..57354152,+p@chr8:57354143..57354152
+
Hg19::chr8:57354182..57354206,+p@chr8:57354182..57354206
+
Hg19::chr8:57354186..57354207,-p@chr8:57354186..57354207
-
Hg19::chr8:57354211..57354220,+p@chr8:57354211..57354220
+
Hg19::chr8:57354215..57354233,-p@chr8:57354215..57354233
-
Hg19::chr8:57354251..57354262,-p@chr8:57354251..57354262
-
Hg19::chr8:57354262..57354270,+p@chr8:57354262..57354270
+
Hg19::chr8:57354275..57354292,-p@chr8:57354275..57354292
-
Hg19::chr8:57354278..57354286,+p@chr8:57354278..57354286
+
Hg19::chr8:57354303..57354312,-p@chr8:57354303..57354312
-
Hg19::chr8:57354324..57354335,-p@chr8:57354324..57354335
-
Hg19::chr8:57354360..57354367,+p@chr8:57354360..57354367
+
Hg19::chr8:57354463..57354473,+p@chr8:57354463..57354473
+
Hg19::chr8:57358373..57358395,+p1@ENST00000518662
p1@uc003xtb.1
Hg19::chr8:57358393..57358427,-p2@PENK
Hg19::chr8:57358432..57358446,-p3@PENK
Hg19::chr8:57359192..57359208,-p1@PENK
Hg19::chr8:57359452..57359471,-p4@PENK
Hg19::chr8:57359557..57359570,-p5@PENK


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:0014812muscle cell migration0.00638704923454376
GO:0051451myoblast migration0.00638704923454376
GO:0001662behavioral fear response0.00638704923454376
GO:0002209behavioral defense response0.00638704923454376
GO:0001515opioid peptide activity0.00638704923454376
GO:0030878thyroid gland development0.00638704923454376
GO:0048538thymus development0.00638704923454376
GO:0042596fear response0.00638704923454376
GO:0048704embryonic skeletal morphogenesis0.0072992699464958
GO:0033555multicellular organismal response to stress0.00781995564380078
GO:0048706embryonic skeletal development0.00781995564380078
GO:0007600sensory perception0.00781995564380078
GO:0048705skeletal morphogenesis0.00781995564380078
GO:0019233sensory perception of pain0.00781995564380078
GO:0001657ureteric bud development0.00924438094333698
GO:0050877neurological system process0.0102140138971916
GO:0001656metanephros development0.0102140138971916
GO:0045664regulation of neuron differentiation0.0102140138971916
GO:0042472inner ear morphogenesis0.0102140138971916
GO:0042471ear morphogenesis0.0102140138971916
GO:0005184neuropeptide hormone activity0.0102140138971916
GO:0035270endocrine system development0.0102140138971916
GO:0003008system process0.0102140138971916
GO:0030855epithelial cell differentiation0.0102140138971916
GO:0001822kidney development0.0102140138971916
GO:0048839inner ear development0.0102140138971916
GO:0001655urogenital system development0.0102140138971916
GO:0048741skeletal muscle fiber development0.0102140138971916
GO:0048747muscle fiber development0.0102140138971916
GO:0043583ear development0.0102140138971916
GO:0048732gland development0.0108252756003371
GO:0002009morphogenesis of an epithelium0.014359014802047
GO:0007519skeletal muscle development0.0148070772530198
GO:0007423sensory organ development0.0182250738705893
GO:0014706striated muscle development0.0182250738705893
GO:0048598embryonic morphogenesis0.0182250738705893
GO:0009792embryonic development ending in birth or egg hatching0.0182250738705893
GO:0043009chordate embryonic development0.0182250738705893
GO:0007389pattern specification process0.0231686483691839
GO:0050954sensory perception of mechanical stimulus0.0234575397976375
GO:0007605sensory perception of sound0.0234575397976375
GO:0045595regulation of cell differentiation0.024976336011968
GO:0007218neuropeptide signaling pathway0.0279938939753307
GO:0007517muscle development0.0279938939753307
GO:0048534hemopoietic or lymphoid organ development0.0279938939753307
GO:0002520immune system development0.0288061754355248
GO:0001501skeletal development0.0309625857559595
GO:0005667transcription factor complex0.0309625857559595
GO:0030182neuron differentiation0.0309625857559595
GO:0032501multicellular organismal process0.0309625857559595
GO:0005179hormone activity0.0309625857559595
GO:0016477cell migration0.0312158469806535
GO:0005625soluble fraction0.0312158469806535
GO:0009790embryonic development0.0312158469806535
GO:0050793regulation of developmental process0.0312158469806535
GO:0048699generation of neurons0.0314350865926451
GO:0022008neurogenesis0.0334260794360214
GO:0007610behavior0.0368445245302705
GO:0009887organ morphogenesis0.0445526366657958
GO:0051674localization of cell0.0455775334293007
GO:0006928cell motility0.0455775334293007



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
non-terminally differentiated cell4.72e-14180
fibroblast2.26e-1075
Uber Anatomy
Ontology termp-valuen
adult organism1.17e-22115
neural tube1.04e-1857
neural rod1.04e-1857
future spinal cord1.04e-1857
neural keel1.04e-1857
regional part of nervous system4.55e-1894
nervous system4.55e-1894
central nervous system2.49e-1782
neurectoderm3.24e-1690
regional part of forebrain9.54e-1641
forebrain9.54e-1641
future forebrain9.54e-1641
neural plate1.97e-1586
presumptive neural plate1.97e-1586
regional part of brain2.24e-1559
ectoderm4.10e-15173
presumptive ectoderm4.10e-15173
anterior neural tube6.00e-1542
anterior region of body7.51e-15129
craniocervical region7.51e-15129
head1.07e-14123
ectoderm-derived structure2.32e-14169
gray matter5.88e-1334
brain grey matter5.88e-1334
telencephalon1.40e-1234
cerebral hemisphere1.45e-1232
brain1.80e-1269
future brain1.80e-1269
organism subdivision2.69e-12365
regional part of telencephalon2.92e-1233
pre-chordal neural plate9.74e-1261
multi-cellular organism1.48e-10659
cerebral cortex1.21e-0825
pallium1.21e-0825
regional part of cerebral cortex1.35e-0822
multi-tissue structure2.43e-08347
neocortex4.39e-0820
anatomical group2.85e-07626
anatomical system3.72e-07625
surface structure4.74e-0795
anatomical cluster5.48e-07286
somite6.68e-0783
paraxial mesoderm6.68e-0783
presomitic mesoderm6.68e-0783
presumptive segmental plate6.68e-0783
trunk paraxial mesoderm6.68e-0783
presumptive paraxial mesoderm6.68e-0783


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

This analysis result is provided for C0 - C305 clusters.

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