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Coexpression cluster:C566: Difference between revisions

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|pathway_enrichment=4.88436109433595e-05;0.00386475071589332;2;200;Focal adhesion (KEGG):04510!8.76239653607e-06;0.00110931940146646;2;85;ECM-receptor interaction (KEGG):04512!7.95242710836606e-06;0.00110931940146646;2;81;Protein digestion and absorption (KEGG):04974!1.36590298944621e-05;0.00144102765386575;2;106;Amoebiasis (KEGG):05146!0.000130824789291056;0.00752837196556711;2;327;Pathways in cancer (KEGG):05200!8.76239653607e-06;0.00110931940146646;2;85;Small cell lung cancer (KEGG):05222!4.31443715156972e-05;0.00386475071589332;2;188;Focal Adhesion (Wikipathways):WP306!8.76239653607e-06;0.00110931940146646;2;85;Integrin cell surface interactions (Reactome):REACT_13552!5.10526184734612e-06;0.00110931940146646;2;65;Signaling by PDGF (Reactome):REACT_16888!8.58567593366187e-05;0.00603859207334218;2;265;Axon guidance (Reactome):REACT_18266!0.000816154648788236;0.0430521577235794;2;816;TGF beta receptor up reg. targets (Netpath):NetPath_7!0.000101437625782269;0.00642100171201764;2;288;{ACTB,297} (Static Module):NA
|pathway_enrichment=4.88436109433595e-05;0.00386475071589332;2;200;Focal adhesion (KEGG):04510!8.76239653607e-06;0.00110931940146646;2;85;ECM-receptor interaction (KEGG):04512!7.95242710836606e-06;0.00110931940146646;2;81;Protein digestion and absorption (KEGG):04974!1.36590298944621e-05;0.00144102765386575;2;106;Amoebiasis (KEGG):05146!0.000130824789291056;0.00752837196556711;2;327;Pathways in cancer (KEGG):05200!8.76239653607e-06;0.00110931940146646;2;85;Small cell lung cancer (KEGG):05222!4.31443715156972e-05;0.00386475071589332;2;188;Focal Adhesion (Wikipathways):WP306!8.76239653607e-06;0.00110931940146646;2;85;Integrin cell surface interactions (Reactome):REACT_13552!5.10526184734612e-06;0.00110931940146646;2;65;Signaling by PDGF (Reactome):REACT_16888!8.58567593366187e-05;0.00603859207334218;2;265;Axon guidance (Reactome):REACT_18266!0.000816154648788236;0.0430521577235794;2;816;TGF beta receptor up reg. targets (Netpath):NetPath_7!0.000101437625782269;0.00642100171201764;2;288;{ACTB,297} (Static Module):NA
|tfbs_overrepresentation=0.209126,0.275631,0.0421171,0.229529,0.695328,0.000582309,0.208995,0.0700519,0.0139964,0.129676,0.551034,0.394962,0.102778,0.162131,0.576196,0.288795,0.0489415,0.423786,0.251434,0.125167,0.00574307,0.531657,0.366297,0.412439,0.202647,0.042538,0.356469,0.0149409,0.562936,0.407128,0.345749,0.137206,0.0924848,0.130488,0.0529683,0.375429,0.099527,0.208823,0.495358,0.308005,0.417894,0.124451,0.0480903,0.0246206,0.151416,0.178709,0.186745,0.0932714,0.466985,0.497953,0.0616071,0.257015,0.0583615,0.40582,0.330863,0.0190105,0.454628,0.00203117,0.35273,0.120273,0.147274,0.578152,0.126247,0.0673426,0.258646,0.241421,0.0308569,0.281114,0.381229,0.0757353,0.0447639,0.311847,0.391856,0.492388,0.0392318,0.0879723,0.102941,0.212019,0.18328,0.0380772,0.101337,0.746552,0.206756,0.478285,0.279196,0.787192,0.298609,0.13168,0.238816,0.047593,0.380089,0.237575,0.414114,0.228054,0.0830247,0.139211,0.0496742,4.03707e-05,0.404948,0.245079,0.270762,0.821668,0.557812,0.182452,0.0450043,0.199788,0.0536435,0.180789,0.0519233,0.49849,0.29193,0.168457,0.0117525,0.0907785,0.111855,0.167333,0.103799,0.00397971,0.549916,0.373123,0.254185,0.369298,0.552981,0.00149236,0.437844,0.278349,0.0923406,0.0764104,0.375023,0.00808459,0.279352,0.0655751,0.26965,0.115676,0.00087343,0.456727,0.300698,0.261847,0.164052,0.0209147,0.115627,0.0376461,0.343262,0.229177,0.117323,0.318275,0.107302,0.374539,0.190907,0.496831,0.00760131,0.562745,0.000813245,0.133842,0.207678,0.486726,0.339268,0.749117,0.246562,0.167207,0.74796,0.41377,0.029622,0.573827,0.0298656,0.476513,0.195791,0.165111,0.197229,0.142011,0.0909588,0.187726,0.425328,0.25683,0.0105156,0.39556,0.553565,0.0936632,0.649476,0.175944,0.0146021,0.501819,0.00995544,0.480568,0.335318,0.147092,0.659776,0.0206968,0.0787222,0.00392219,0.123363,0.303195,0.155664,0.749857,0.47141,0.226754,0.352463,0.282243,0.311735,0.128382,0.392802,0.2827,0.153822,0.0446476,0.542704,0.0790409,0.508206,0.00211272,0.127582,0.649271,0.000134203,0.117902,0.0327903,0.472137,0.14269,7.71479e-05,0.615816,0.433065,0.29321,0.00297254,0.557966,0.452327,0.0636709,0.00277474,0.335836,0.163486,0.549445,0.380871,0.0444435,0.280653,0.00664555,0.00522622,0.203837,0.345882,0.41597,0.406517,0.227421,0.223952,0.614095,0.00214511,0.00493478,0.00914235,0.424459,0.370391,0.141787,0.543795,0.0764355,0.132344,0.710227,0.00478567,0.603019,0.0979981,0.0254392,0.423197,0.00247566,0.23771,0.123554,0.69956,0.00712854,0.00109191,0.288882,0.641789,0.0715764,0.166674,0.170824,0.0756962,0.363298,0.0948199,0.00494681,0.342148,0.00889407,0.00545356,0.0745126,0.0015989,0.383097,0.0186638,0.171164,0.0496926,0.350991,0.82189,0.451792,0.451809,0.32494,0.268434,0.640336,0.435775,0.801526,0.211019,0.0417171,0.138052,0.0310514,0.00649079,0.006451,0.628656,0.119243,0.252736,0.0291582,0.0395836,0.00774654,0.137147,0.020794,0.862067,0.303085,0.0963099,0.00484187,0.175075,0.0252862,0.169559,0.0444763,0.179758,0.0148417,0.42362,0.323769,0.568053,0.750393,0.448679,0.00924746,0.146915,0.206297,0.0975119,0.570753,0.0269659,0.00493722,0.154347,0.174406,0.0636091,0.831311,0.145743,0.0449267,0.0114419,0.0160115,0.1799,0.0719378,0.282252,0.136408,0.000371498,0.24179,0.313642,0.385295,0.658307,0.635933,0.31577,0.600744,0.82052,0.0158472,0.665578,0.194057,0.584043,0.000366869,0.426865,0.511987,0.0953133,0.000801678,0.197353,0.0338409,0.130732,0.0161034,0.309372,0.332899,0.297189,0.0582891,0.0123979,0.0994576,0.0686311,0.00126201,0.0287094,0.259562,0.213974,0.0111813,0.0165908,0.108994,0.0257574,0.339244,2.0729e-06,0.11448,0.201756,0.0835614,0.555361,0.0270074,0.0622504,0.274912,0.0634142,0.575024,0.82405,0.176838,0.0824677,0.401513,0.177976,0.328072,0.596068,0.0164005,0.334558,0.0273241,0.0100926,0.0440554,0.471679,0.886582,0.0524796,0.205235,0.017081,0.246033,0.015813,0.0193322,0.203855,0.0126648,0.224579,0.000168264,0.00604711,0.537988,0.0187751,0.0284437,0.553172,0.265674,0.0271804,0.310455,0.57931,0.542866,0.886493,0.00745004,0.106536,0.222917,0.0110186,0.397098,0.303084,0.00291272,8.84117e-06,0.00736879,0.333975,0.708216,0.210942,0.333282,0.810429,0.235616,0.380032,0.00471497,0.259384,0.557494,0.628564,0.102506,0.60444,0.000137426,0.106633,0.168818,0.673932,0.39222,0.279289,0.210248,0.159097,0.397423,0.010066,0.083345,0.0605599,0.146941,0.636322,0.00848416,0.147777,0.320036,0.263295,0.107899,0.35151,0.0406082,0.202485,0.154167,0.70315,0.0964858,0.377154,0.313969,0.132916,0.275185,0.211334,0.0140949,0.00637599,0.181378,0.122861,0.24352,3.09549e-05,0.0462535,0.0918879,0.305024,0.522274,0.740189,0.224195,0.628872,0.477458,0.118295,0.395116,0.38348,0.604976,0.453504,0.212764,0.0205756,0.505197,0.168961,0.716255,0.68276,0.028278,0.239235,0.369672,0.30797,0.290939,0.466967,0.147729,0.172509,0.686758,0.530571,0.0057513,0.23153,0.00748611,0.00778049,0.517611,0.0861027,0.296452,0.627991,0.386878,0.413594,0.0585847,0.0473786,0.123162,0.511987,0.0254043,0.27073,0.0490656,0.718595,0.150264,0.528693,0.215657,0.249369,0.00911066,0.0128167,0.0735767,0.421121,0.6057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|tfbs_overrepresentation_for_novel_motifs=0.157827,0.0158194,0.464859,0.718081,0.789854,0.25764,0.318839,1.23744,1.22427,0.654939,0.234283,0.355038,0.0400361,0.309388,0.393521,0.431887,1.27402,1.06688,0.171822,0.520625,0.907313,0.081539,0.251588,0.387475,0.542899,0.977358,0.89505,0.249905,0.798464,0.274385,0.622094,1.34484,0.260283,1.01329,0.104423,0.579385,0.102549,0.258546,0.299553,0.188103,0.690753,0.593399,0.373399,0.123709,0.321633,0.173971,0.319738,0.226038,0.541305,0.798822,0.386472,0.329494,0.0752075,0.615394,1.79167,0.311792,0.407898,0.2852,0.814637,0.776377,0.582323,0.321692,1.22686,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,1.08274,0.0621482,0.614975,0.756844,0.347788,0.580064,0.120629,0.471562,0.532468,0.18023,0.400226,0.48568,0.336303,0.219253,0.70821,0.588509,0.514277,0.263815,0.408949,1.29895,0.932961,0.68283,0.560183,0.0788172,0.791919,0.60642,0.169943,0.599297,0.412954,0.229879,0.301599,0.555021,0.594155,1.28107,0.445845,0.652834,0.500571,0.306566,0.18443,0.115618,0.160439,0.591605,0.455599,0.241506,0.886618,0.101627,0.704262,0.216858,0.453946,0.578957,0.748992,0.406842,0.71014,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.0864157,0.683478,0.627156,0.803201,0.342946,0.945426,0.249246,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,1.52766,0.596045,1.13655,0.76278,0.432737,1.59165,0.203207,0.266036,1.19009,0.806242,0.683836,0.774617,0.321292,1.07219,0.394947,0.751217,0.184652,0.164414,0.867287,0.66649,0.531753,0.166635,0.46162,0.335644,0.0708512,0.317742,0.297192
}}
}}

Revision as of 14:18, 26 November 2012


Full id: C566_Pericytes_Renal_hepatic_Fibroblast_Endothelial_Hepatic_Lens



Phase1 CAGE Peaks

Hg19::chr13:110802350..110802403,-p3@COL4A1
Hg19::chr13:110802503..110802522,-p9@COL4A1
Hg19::chr13:110802740..110802769,-p2@COL4A1
Hg19::chr13:110804802..110804837,-p@chr13:110804802..110804837
-
Hg19::chr13:110829310..110829326,-p@chr13:110829310..110829326
-
Hg19::chr13:110829341..110829354,-p@chr13:110829341..110829354
-
Hg19::chr13:110839601..110839634,-p@chr13:110839601..110839634
-
Hg19::chr13:110853822..110853836,-p@chr13:110853822..110853836
-
Hg19::chr13:110861222..110861235,-p@chr13:110861222..110861235
-
Hg19::chr13:110864247..110864268,-p@chr13:110864247..110864268
-
Hg19::chr13:110959496..110959511,-p1@COL4A1
Hg19::chr13:110959598..110959611,+p2@COL4A2
Hg19::chr13:110959623..110959640,+p1@COL4A2
Hg19::chr13:111009846..111009888,-p@chr13:111009846..111009888
-
Hg19::chr13:111164370..111164403,+p@chr13:111164370..111164403
+
Hg19::chr13:111164549..111164576,+p@chr13:111164549..111164576
+


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
4.88436109433595e-050.003864750715893322200Focal adhesion (KEGG):04510
8.76239653607e-060.00110931940146646285ECM-receptor interaction (KEGG):04512
7.95242710836606e-060.00110931940146646281Protein digestion and absorption (KEGG):04974
1.36590298944621e-050.001441027653865752106Amoebiasis (KEGG):05146
0.0001308247892910560.007528371965567112327Pathways in cancer (KEGG):05200
8.76239653607e-060.00110931940146646285Small cell lung cancer (KEGG):05222
4.31443715156972e-050.003864750715893322188Focal Adhesion (Wikipathways):WP306
8.76239653607e-060.00110931940146646285Integrin cell surface interactions (Reactome):REACT_13552
5.10526184734612e-060.00110931940146646265Signaling by PDGF (Reactome):REACT_16888
8.58567593366187e-050.006038592073342182265Axon guidance (Reactome):REACT_18266
0.0008161546487882360.04305215772357942816TGF beta receptor up reg. targets (Netpath):NetPath_7
0.0001014376257822690.006421001712017642288{ACTB,297} (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:0005581collagen9.1276660944864e-05
GO:0005604basement membrane9.1276660944864e-05
GO:0005201extracellular matrix structural constituent0.00013724278986645
GO:0044420extracellular matrix part0.00013724278986645
GO:0006817phosphate transport0.00013724278986645
GO:0015698inorganic anion transport0.000379277449588247
GO:0006820anion transport0.000502106119333132
GO:0005578proteinaceous extracellular matrix0.000746924249734859
GO:0005587collagen type IV0.00127548516830642
GO:0030935sheet-forming collagen0.00137750370557821
GO:0044421extracellular region part0.00254125210080381
GO:0016525negative regulation of angiogenesis0.003251912687054
GO:0006811ion transport0.00483283573650064
GO:0045765regulation of angiogenesis0.0062286291620965
GO:0030198extracellular matrix organization and biogenesis0.00703642914021911
GO:0043062extracellular structure organization and biogenesis0.0120393189222703
GO:0001525angiogenesis0.0173898289872081
GO:0048514blood vessel morphogenesis0.0181053237656383
GO:0048646anatomical structure formation0.0181053237656383
GO:0001568blood vessel development0.0181053237656383
GO:0001944vasculature development0.0181053237656383
GO:0006810transport0.0250029879971245
GO:0051234establishment of localization0.0251161640147931
GO:0051179localization0.0282668149955082
GO:0009887organ morphogenesis0.0330695538606439



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
vasculature2.70e-1778
vascular system2.70e-1778
epithelial tube2.79e-16117
circulatory system9.65e-16112
cardiovascular system5.00e-15109
splanchnic layer of lateral plate mesoderm6.64e-1483
vessel1.00e-1368
mesenchyme6.40e-13160
entire embryonic mesenchyme6.40e-13160
epithelial tube open at both ends1.87e-1059
blood vessel1.87e-1059
blood vasculature1.87e-1059
vascular cord1.87e-1059
trunk mesenchyme8.10e-10122
epithelial vesicle1.45e-0978
muscle tissue1.46e-0964
musculature1.46e-0964
musculature of body1.46e-0964
skeletal muscle tissue3.46e-0962
striated muscle tissue3.46e-0962
myotome3.46e-0962
trunk3.86e-09199
compound organ4.44e-0968
nephron epithelium1.53e-0815
renal tubule1.53e-0815
nephron tubule1.53e-0815
nephron1.53e-0815
uriniferous tubule1.53e-0815
nephrogenic mesenchyme1.53e-0815
excretory tube1.60e-0816
kidney epithelium1.60e-0816
parenchyma5.55e-0815
unilaminar epithelium9.02e-08148
organism subdivision1.43e-07264
mesoderm3.75e-07315
mesoderm-derived structure3.75e-07315
presumptive mesoderm3.75e-07315
artery5.77e-0742
arterial blood vessel5.77e-0742
arterial system5.77e-0742
dense mesenchyme tissue6.75e-0773
urogenital ridge6.85e-0711
cortex of kidney6.85e-0712
renal parenchyma6.85e-0712
somite7.35e-0771
presomitic mesoderm7.35e-0771
presumptive segmental plate7.35e-0771
dermomyotome7.35e-0771
trunk paraxial mesoderm7.35e-0771
abdominal segment of trunk8.28e-0760
abdomen8.28e-0760


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.