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Coexpression cluster:C1435: Difference between revisions

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|full_id=C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus
|full_id=C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus
|id=C1435
|id=C1435
|ontology_enrichment_celltype=CL:0002139!6.63e-12!24;CL:0000115!1.02e-11!35;CL:0002078!9.37e-11!44;CL:0000213!9.01e-10!57;CL:0000215!9.01e-10!57;CL:0000071!1.04e-08!18;CL:0002546!1.04e-08!18
|ontology_enrichment_celltype=CL:0000115!1.12e-14!36;CL:0002139!9.80e-14!24;CL:0002078!1.35e-12!45;CL:0000213!1.30e-10!58;CL:0000215!1.30e-10!58;CL:0000071!9.21e-10!18;CL:0002546!9.21e-10!18
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.32e-31!115;UBERON:0004111!3.00e-24!241;UBERON:0000025!1.16e-23!194;UBERON:0000119!2.80e-21!312;UBERON:0000483!4.81e-21!309;UBERON:0000477!6.72e-21!286;UBERON:0000073!5.06e-17!94;UBERON:0001016!5.06e-17!94;UBERON:0005743!1.41e-15!86;UBERON:0002346!2.60e-15!90;UBERON:0001017!3.47e-15!82;UBERON:0000468!2.22e-14!659;UBERON:0001049!2.62e-14!57;UBERON:0005068!2.62e-14!57;UBERON:0006241!2.62e-14!57;UBERON:0007135!2.62e-14!57;UBERON:0003075!4.15e-14!86;UBERON:0007284!4.15e-14!86;UBERON:0000955!5.83e-12!69;UBERON:0006238!5.83e-12!69;UBERON:0002616!6.53e-12!59;UBERON:0003914!6.97e-12!118;UBERON:0003080!1.90e-11!42;UBERON:0000475!3.87e-11!365;UBERON:0002780!6.65e-11!41;UBERON:0001890!6.65e-11!41;UBERON:0006240!6.65e-11!41;UBERON:0000467!7.99e-11!625;UBERON:0000480!1.02e-10!626;UBERON:0000481!1.85e-10!347;UBERON:0003056!6.13e-10!61;UBERON:0000922!8.01e-10!612;UBERON:0001893!1.17e-09!34;UBERON:0004872!1.86e-09!84;UBERON:0002020!2.32e-09!34;UBERON:0003528!2.32e-09!34;UBERON:0002791!2.67e-09!33;UBERON:0000924!4.66e-09!173;UBERON:0006601!4.66e-09!173;UBERON:0001869!5.50e-09!32;UBERON:0000064!8.65e-09!219;UBERON:0000055!9.21e-09!69;UBERON:0001986!1.04e-08!18;UBERON:0004638!1.04e-08!18;UBERON:0004852!1.04e-08!18;UBERON:0002050!2.52e-08!605;UBERON:0005423!2.52e-08!605;UBERON:0004121!3.22e-08!169;UBERON:0002049!4.58e-08!79;UBERON:0007798!4.58e-08!79;UBERON:0000923!5.03e-08!604;UBERON:0005291!5.03e-08!604;UBERON:0006598!5.03e-08!604;UBERON:0002532!5.03e-08!604;UBERON:0003103!7.49e-08!69;UBERON:0002619!8.30e-08!22;UBERON:0001950!2.67e-07!20;UBERON:0000956!3.71e-07!25;UBERON:0000203!3.71e-07!25;UBERON:0001981!3.82e-07!60;UBERON:0007500!3.82e-07!60;UBERON:0004537!3.82e-07!60;UBERON:0006965!3.82e-07!60;UBERON:0000153!4.57e-07!129;UBERON:0007811!4.57e-07!129
|ontology_enrichment_uberon=UBERON:0007023!7.87e-34!114;UBERON:0000477!7.17e-22!373;UBERON:0004111!4.89e-19!240;UBERON:0000025!1.13e-18!192;UBERON:0000119!3.65e-13!309;UBERON:0000483!6.33e-13!306;UBERON:0000468!5.30e-12!656;UBERON:0001016!1.42e-11!89;UBERON:0002346!1.13e-10!86;UBERON:0001049!1.73e-10!56;UBERON:0005068!1.73e-10!56;UBERON:0006241!1.73e-10!56;UBERON:0007135!1.73e-10!56;UBERON:0001017!3.08e-10!81;UBERON:0011216!3.28e-10!223;UBERON:0003914!5.28e-10!117;UBERON:0004638!9.21e-10!18;UBERON:0001986!9.21e-10!18;UBERON:0004852!9.21e-10!18;UBERON:0000073!1.95e-09!53;UBERON:0002616!1.95e-09!53;UBERON:0003075!2.19e-09!82;UBERON:0007284!2.19e-09!82;UBERON:0010314!1.48e-08!132;UBERON:0002780!1.71e-08!41;UBERON:0001890!1.71e-08!41;UBERON:0003080!1.71e-08!41;UBERON:0006240!1.71e-08!41;UBERON:0000467!2.16e-08!624;UBERON:0000480!2.90e-08!625;UBERON:0000955!4.92e-08!68;UBERON:0006238!4.92e-08!68;UBERON:0000922!7.10e-08!592;UBERON:0000481!7.42e-08!342;UBERON:0003103!9.94e-08!68;UBERON:0004872!9.98e-08!83;UBERON:0000055!1.47e-07!68;UBERON:0000487!2.24e-07!22;UBERON:0006914!4.43e-07!25;UBERON:0000923!5.23e-07!560;UBERON:0010316!5.23e-07!560;UBERON:0005291!5.23e-07!560;UBERON:0006598!5.23e-07!560;UBERON:0010317!5.23e-07!560;UBERON:0002532!5.23e-07!560;UBERON:0002050!5.92e-07!564;UBERON:0005423!5.96e-07!581;UBERON:0001893!6.43e-07!34
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466065765730013!REST#5978;5:8.04169059677335:6.54774545315482e-05:0.00106186333444416!USF1#7391;5:5.3012493976733:0.000500332754985889:0.00441224796064944
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466065765730013!REST#5978;5:8.04169059677335:6.54774545315482e-05:0.00106186333444416!USF1#7391;5:5.3012493976733:0.000500332754985889:0.00441224796064944
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378417,0.0592343,0.245796,0.0870651,0.101982,0.374106,0.282907,0.153213,0.185351,0.29465,0.231794,0.173078,0.00611106,5.22305e-07,0.000140436,0.00344976,0.0289867,0.127078,0.378656,0.392439,0.153874,0.145835,0.297422,0.349099,0.106792,0.149864,0.109211,0.081783,0.0678906,0.076236,0.444489,0.31161,0.361651,0.0953991,0.319245,5.15953e-05,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.00244756,0.205891,0.207936,0.000412895,0.0563868,9.89644e-07,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.632847,0.102964,0.491614,0.146453,0.315229,0.157053,0.332022,0.00153888,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.00512114,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.000692459,0.0014462,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,4.39089e-07,0.00650982,0.628069,0.387334,0.494914,0.224219,0.347904,0.324262,0.00127806,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.000483593,0.0149147,0.0327122,0.0699003,0.235435,0.31953,0.000517116,3.81694e-07,0.00132063,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,1.2275e-05,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,8.92363e-05,0.3889,0.192889,0.0463105,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.409805,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.255609,0.0157825,0.439697,0.493192,0.223892,0.160738,0.000190924,0.213489,0.000112437,0.338443,0.319005,0.180695,0.00362715,0.436073,0.261316,0.189596,0.00038198,0.196587,0.213353,0.0504588,0.0530893,0.173101,0.0336807,4.00685e-05,0.341713,0.156156,0.33569,0.288104,1.02692e-07,0.174852,0.114697,0.0200942,0.324956,0.388835,0.0163966,0.000748996,0.0469515,0.070868,1.83925e-06,0.245,0.0850317,0.249379,0.00509914,0.60218,0.00754396,0.000750083,0.409327,1.36249e-08,0.685907,0.603176,0.305003,0.000240439,0.355968,0.0824588,0.592254,0.00434194,0.00307631,0.0320331,0.0586453,0.0011161,0.0159712,1.03533e-06,0.0119872,0.750579,0.689958,0.772379,3.98225e-09,2.63188e-05,0.402631,0.000799452,0.0139712,7.21997e-05,0.488239,0.00326138,0.476894,0.48468,0.494578,0.301433,0.00890326,0.00517823,1.25588e-05,0.00223773,0.559471,0.360334,0.449761,0.6937,0.427531,0.0011142,0.00353551,2.25201e-05,4.52622e-10,0.297082,3.51716e-05,9.41394e-11,9.21968e-05,0.000133253,0.240506,0.000358733,0.72684,8.66559e-05,0.000573639,2.88866e-06,0.36546,0.360788,0.368898,0.510705,0.447298,0.670481,0.576455,8.04961e-06,0.287839,0.262665,0.000120132,0.183051,0.530004,0.0123228,0.300816,1.27445e-11,0.225997,0.487688,9.431e-06,0.529993,0.329919,0.484887,0.086793,0.0454127,0.650025,0.766238,0.540605,9.08876e-09,0.563634,2.84791e-05,0.624569,0.435062,1.70742e-06,5.18811e-06,0.394773,0.659669,0.659285,0.00890582,8.36454e-07,1.40397e-05,0.367684,0.700165,0.258457,3.75931e-11,0.305952,0.356524,0.159817,0.0419695,0.145279,0.319704,0.194695,0.607569,0.000157173,0.00451034,0.000363535,0.198803,9.64299e-06,0.594475,0.416321,0.365565,1.00869e-10,0.24311,0.0323424,0.578885,0.474879,0.148175,0.000946778,0.424119,0.60488,0.519279,0.515179,0.39773,0.623664,0.000672353,0.438945,0.619652,0.706112,0.754688,0.39196,1.84688e-05,0.0101665,0.346355,0.712437,0.00065111,0.520214,0.708106,0.486574,0.231819,0.0100546,0.639482,0.471879,0.600697,0.474504,0.621275,0.142884,0.00223672,0.564042,0.356483,0.00319854,0.00334807,0.55481,0.777518,0.509842,8.78725e-06,0.368631,0.321667,0.149733,0.477082,0.078203,0.066291,0.343349,0.000391869,0.341084,0.138667,0.000442332,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.440771,0.613566,0.445744,0.371991,0.694395,0.326635,0.349721,0.39301,0.0147365,0.00170901,0.524829,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.0294624,0.327419,0.402268,0.479755,0.163801,0.245045,0.0120311,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.00411912,0.406219,0.298,0.015951,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.213995,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.011255,0.381922,0.372037,0.263608,0.3488,0.0205291,6.18367e-06,0.00186357,0.431643,0.00689472,0.360691,0.0371914,0.35537,0.0184757,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.0396204,0.482957,0.388728,0.157712,7.99844e-06,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,7.34091e-05,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.491191,0.000258181,0.263371,0.000427379,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,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}}
}}

Revision as of 11:17, 19 October 2012


Full id: C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus



Phase1 CAGE Peaks

Hg19::chr17:40913145..40913205,+p2@RAMP2
Hg19::chr17:40913210..40913221,+p3@RAMP2
Hg19::chr17:40913222..40913233,+p4@RAMP2
Hg19::chr17:40913236..40913252,+p1@RAMP2
Hg19::chr17:40913264..40913273,+p6@RAMP2
Hg19::chr17:72966776..72966789,+p@chr17:72966776..72966789
+


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>

Uber Anatomy
Ontology termp-valuen
adult organism7.87e-34114
anatomical cluster7.17e-22373
anatomical conduit4.89e-19240
tube1.13e-18192
cell layer3.65e-13309
epithelium6.33e-13306
multi-cellular organism5.30e-12656
nervous system1.42e-1189
neurectoderm1.13e-1086
neural tube1.73e-1056
neural rod1.73e-1056
future spinal cord1.73e-1056
neural keel1.73e-1056
central nervous system3.08e-1081
organ system subdivision3.28e-10223
epithelial tube5.28e-10117
blood vessel endothelium9.21e-1018
endothelium9.21e-1018
cardiovascular system endothelium9.21e-1018
regional part of nervous system1.95e-0953
regional part of brain1.95e-0953
neural plate2.19e-0982
presumptive neural plate2.19e-0982
structure with developmental contribution from neural crest1.48e-08132
regional part of forebrain1.71e-0841
forebrain1.71e-0841
anterior neural tube1.71e-0841
future forebrain1.71e-0841
anatomical system2.16e-08624
anatomical group2.90e-08625
brain4.92e-0868
future brain4.92e-0868
embryo7.10e-08592
multi-tissue structure7.42e-08342
compound organ9.94e-0868
splanchnic layer of lateral plate mesoderm9.98e-0883
vessel1.47e-0768
simple squamous epithelium2.24e-0722
squamous epithelium4.43e-0725
germ layer5.23e-07560
germ layer / neural crest5.23e-07560
embryonic tissue5.23e-07560
presumptive structure5.23e-07560
germ layer / neural crest derived structure5.23e-07560
epiblast (generic)5.23e-07560
embryonic structure5.92e-07564
developing anatomical structure5.96e-07581
telencephalon6.43e-0734


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
CTCF#1066443.573504248716680.01316635007238510.0466065765730013
REST#597858.041690596773356.54774545315482e-050.00106186333444416
USF1#739155.30124939767330.0005003327549858890.00441224796064944



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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