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Coexpression cluster:C1489: Difference between revisions

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|full_id=C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum
|full_id=C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum
|id=C1489
|id=C1489
|ontology_enrichment_celltype=CL:0000181!9.33e-09!12;CL:0000417!9.33e-09!12;CL:0000668!9.33e-09!12;CL:0000414!9.33e-09!12;CL:0000412!9.33e-09!12;CL:0000182!9.33e-09!12;CL:0002322!4.48e-08!5
|ontology_enrichment_celltype=CL:0000181!8.86e-20!12;CL:0000417!8.86e-20!12;CL:0000668!8.86e-20!12;CL:0000412!8.86e-20!12;CL:0000182!8.86e-20!12;CL:0000223!9.33e-08!58;CL:0002563!3.13e-07!4
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004921!8.84e-23!129;UBERON:0004185!8.84e-23!129;UBERON:0004119!7.26e-21!169;UBERON:0000925!7.26e-21!169;UBERON:0006595!7.26e-21!169;UBERON:0001007!1.11e-20!155;UBERON:0001555!1.11e-20!155;UBERON:0007026!1.11e-20!155;UBERON:0000077!1.63e-17!130;UBERON:0001041!3.75e-14!98;UBERON:0009497!3.26e-13!25;UBERON:0000015!3.26e-13!25;UBERON:0002423!3.26e-13!25;UBERON:0006235!3.26e-13!25;UBERON:0004161!3.26e-13!25;UBERON:0003929!1.25e-12!54;UBERON:0005057!1.29e-12!26;UBERON:0009854!1.29e-11!23;UBERON:0007023!2.00e-11!115;UBERON:0009856!2.32e-11!26;UBERON:0002107!5.50e-11!19;UBERON:0006925!5.50e-11!19;UBERON:0008836!5.50e-11!19;UBERON:0008835!2.02e-10!22;UBERON:0003894!2.02e-10!22;UBERON:0005911!2.35e-10!82;UBERON:0007499!3.20e-10!25;UBERON:0000466!2.36e-09!126;UBERON:0005172!2.98e-09!55;UBERON:0005173!2.98e-09!55;UBERON:0000065!9.80e-09!53;UBERON:0005177!1.04e-08!107;UBERON:0001737!1.27e-08!9;UBERON:0000481!2.01e-08!347;UBERON:0003104!2.69e-08!238;UBERON:0009142!2.69e-08!238;UBERON:0002368!2.80e-08!35;UBERON:0005409!4.09e-08!35;UBERON:0001004!7.59e-08!72;UBERON:0002417!9.93e-08!61;UBERON:0000916!9.93e-08!61;UBERON:0001048!1.04e-07!168;UBERON:0001557!1.09e-07!19;UBERON:0002365!1.39e-07!31;UBERON:0002330!1.39e-07!31;UBERON:0000160!1.64e-07!27;UBERON:0000059!2.37e-07!11;UBERON:0002530!3.14e-07!59;UBERON:0000468!3.95e-07!659;UBERON:0000922!4.12e-07!612
|ontology_enrichment_uberon=UBERON:0000160!1.58e-34!17;UBERON:0005409!3.54e-28!25;UBERON:0009854!3.98e-22!23;UBERON:0002107!1.50e-21!19;UBERON:0006925!1.50e-21!19;UBERON:0008836!1.50e-21!19;UBERON:0000059!7.41e-21!11;UBERON:0004921!4.37e-20!118;UBERON:0009856!2.09e-19!26;UBERON:0008835!1.87e-18!22;UBERON:0003894!1.87e-18!22;UBERON:0001155!4.99e-18!9;UBERON:0001007!2.67e-17!145;UBERON:0001555!2.67e-17!145;UBERON:0007026!2.67e-17!145;UBERON:0007499!4.24e-16!25;UBERON:0009497!4.24e-16!25;UBERON:0000015!4.24e-16!25;UBERON:0002423!4.24e-16!25;UBERON:0006235!4.24e-16!25;UBERON:0004161!4.24e-16!25;UBERON:0004119!2.79e-15!160;UBERON:0000925!2.79e-15!160;UBERON:0006595!2.79e-15!160;UBERON:0003929!3.35e-15!54;UBERON:0002368!5.82e-14!35;UBERON:0002365!9.38e-13!31;UBERON:0002330!9.38e-13!31;UBERON:0005172!1.00e-12!54;UBERON:0005173!1.00e-12!54;UBERON:0002108!1.40e-12!4;UBERON:0004907!4.82e-12!5;UBERON:0002417!2.98e-11!60;UBERON:0000916!2.98e-11!60;UBERON:0000949!1.56e-10!45;UBERON:0011216!1.33e-09!223;UBERON:0002530!1.77e-09!59;UBERON:0005911!3.05e-09!82;UBERON:0001154!9.72e-08!1;UBERON:0001153!9.72e-08!1;UBERON:0001045!9.72e-08!1;UBERON:0001052!2.84e-07!4;UBERON:0001242!3.13e-07!4;UBERON:0001262!3.13e-07!4;UBERON:0004786!3.13e-07!4;UBERON:0004808!3.13e-07!4;UBERON:0001277!3.13e-07!4;UBERON:0005177!4.44e-07!101;UBERON:0000481!4.94e-07!342
|tf_chipseq_enrich=HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209532912822657
|tf_chipseq_enrich=HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209532912822657
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81783,0.0678906,0.076236,0.444489,0.31161,0.361651,0.0953991,0.319245,0.603631,0.0650516,0.575882,0.0889286,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.454529,0.0563868,0.796918,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.632847,0.417985,0.491614,0.146453,0.0559261,0.0130345,0.332022,0.19701,0.0413973,0.262915,0.000559394,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.674943,0.3342,0.100989,0.188919,0.00492272,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.504405,0.628069,0.0871672,0.494914,0.224219,0.347904,0.324262,0.795569,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.712551,0.973581,0.370285,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.0941132,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,0.35188,0.3889,0.192889,0.547162,0.316041,0.203431,0.00463916,0.121421,0.346061,0.275075,0.754571,0.287361,0.138613,0.175356,0.116846,0.267784,0.0430091,0.185281,0.286026,0.31159,0.349805,0.255609,0.0956849,0.439697,0.493192,0.223892,0.160738,0.553042,0.213489,0.212611,0.338443,0.319005,0.180695,0.126288,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.259063,0.306056,0.341713,0.156156,0.33569,0.288104,0.526446,0.761719,0.114697,0.433479,0.324956,0.388835,0.408751,0.648685,0.855529,0.070868,0.654476,0.245,0.0850317,0.249379,0.661446,0.60218,0.11882,0.648789,0.409327,0.466607,0.322166,0.603176,0.101812,0.334228,0.355968,0.636386,0.226461,0.27962,0.616927,0.82397,0.611131,0.312447,0.255628,0.260486,0.387005,0.750579,0.689958,0.435483,0.599685,0.983425,0.402631,0.429394,0.302735,0.623606,0.488239,0.754734,0.218104,0.2667,0.494578,0.301433,0.711296,0.148546,0.819065,0.727698,0.00985896,0.0395776,0.449761,0.331289,0.427531,0.353735,0.629087,0.495268,0.668933,0.297082,0.526245,0.8738,0.746016,0.622334,0.240506,0.369581,0.72684,0.810134,0.144373,0.948012,0.0111953,0.0747286,0.0784093,0.160962,0.447298,0.304675,0.576455,0.619669,0.287839,0.262665,0.0920238,0.183051,0.530004,0.583703,0.300816,0.0976418,0.225997,0.487688,0.491994,0.0411734,0.329919,0.00477506,0.189506,0.300668,0.650025,0.179563,0.540605,0.629269,0.0517235,0.848142,0.256767,0.185857,0.834029,0.455987,0.394773,0.659669,0.0949382,0.711322,0.929537,0.516717,0.367684,0.700165,0.258457,0.893393,0.00618933,0.356524,0.159817,0.532764,0.376842,0.0576354,0.555004,0.607569,0.773067,0.283145,0.231104,0.452272,0.628973,0.594475,0.102066,0.365565,0.47205,0.0156647,0.0323424,0.578885,0.0276985,0.868553,0.518205,0.424119,0.0149171,0.519279,0.515179,0.745866,0.623664,0.414645,0.438945,0.251982,0.346229,0.754688,0.0894513,0.172059,0.355152,0.346355,0.712437,0.0115123,0.520214,0.348678,0.486574,0.231819,0.366382,0.639482,0.471879,0.600697,0.474504,0.253554,0.142884,0.589415,0.202106,0.356483,0.120876,0.0764807,0.55481,0.777518,0.509842,0.597297,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,0.0681033,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.115749,0.613566,0.445744,0.371991,0.694395,0.326635,0.349721,0.39301,0.396235,0.0527577,0.171264,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.139798,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.0963341,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.130527,0.362561,0.213995,0.285875,0.225945,0.018816,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.122302,0.521039,0.328594,0.0482846,0.448388,0.278746,0.000156175,0.232479,0.00833237,0.336321,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.0562621,0.360691,0.26003,0.35537,0.423126,0.0463025,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.124171,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.0113565,0.504058,0.491191,0.210178,0.263371,0.457065,0.0222656,0.0744514,0.403229,0.507716,0.442751,0.323763,0.004871,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.00857271,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.142644,0.486223,0.437432,0.302171,0.0925994,0.00109207,0.00136487,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.132855,0.137165,0.0262964,0.191837,0.0146518,0.0581034,0.289812,0.384881,0.116282,0.369492,0.592234
}}
}}

Revision as of 11:21, 19 October 2012


Full id: C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum



Phase1 CAGE Peaks

Hg19::chr21:44859375..44859383,-p@chr21:44859375..44859383
-
Hg19::chr2:88425813..88425828,-p2@BX641099
Hg19::chr2:88425833..88425845,-p1@BX641099
Hg19::chr2:88427571..88427590,-p1@FABP1
Hg19::chr3:195943369..195943392,+p2@OSTalpha
Hg19::chr5:66307148..66307152,-p@chr5:66307148..66307152
-


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


No GOStat results

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
metabolising cell8.86e-2012
endopolyploid cell8.86e-2012
parenchymal cell8.86e-2012
polyploid cell8.86e-2012
hepatocyte8.86e-2012
endodermal cell9.33e-0858
intestinal epithelial cell3.13e-074
Uber Anatomy
Ontology termp-valuen
intestine1.58e-3417
gastrointestinal system3.54e-2825
digestive tract diverticulum3.98e-2223
liver1.50e-2119
digestive gland1.50e-2119
liver bud1.50e-2119
large intestine7.41e-2111
subdivision of digestive tract4.37e-20118
sac2.09e-1926
hepatic diverticulum1.87e-1822
liver primordium1.87e-1822
colon4.99e-189
digestive system2.67e-17145
digestive tract2.67e-17145
primitive gut2.67e-17145
epithelial sac4.24e-1625
epithelium of foregut-midgut junction4.24e-1625
anatomical boundary4.24e-1625
hepatobiliary system4.24e-1625
foregut-midgut junction4.24e-1625
septum transversum4.24e-1625
endoderm-derived structure2.79e-15160
endoderm2.79e-15160
presumptive endoderm2.79e-15160
gut epithelium3.35e-1554
endocrine gland5.82e-1435
exocrine gland9.38e-1331
exocrine system9.38e-1331
abdomen element1.00e-1254
abdominal segment element1.00e-1254
small intestine1.40e-124
lower digestive tract4.82e-125
abdominal segment of trunk2.98e-1160
abdomen2.98e-1160
endocrine system1.56e-1045
organ system subdivision1.33e-09223
gland1.77e-0959
endo-epithelium3.05e-0982
vermiform appendix9.72e-081
caecum9.72e-081
midgut9.72e-081
rectum2.84e-074
intestinal mucosa3.13e-074
wall of intestine3.13e-074
gastrointestinal system mucosa3.13e-074
gastrointestinal system epithelium3.13e-074
intestinal epithelium3.13e-074
trunk region element4.44e-07101
multi-tissue structure4.94e-07342


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
HEY1#2346253.366759202588090.004423827045203030.0209532912822657



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.