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Coexpression cluster:C540: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003102!5.65e-10!99;UBERON:0000479!9.76e-10!773;UBERON:0007100!1.83e-09!27;UBERON:0007023!1.01e-08!114;UBERON:0000948!5.78e-08!24;UBERON:0005498!5.78e-08!24;UBERON:0004140!5.78e-08!24;UBERON:0009881!5.78e-08!24;UBERON:0004141!5.78e-08!24;UBERON:0003084!5.78e-08!24;UBERON:0007005!5.78e-08!24;UBERON:0004139!5.78e-08!24;UBERON:0004291!5.78e-08!24;UBERON:0001013!6.18e-08!14;UBERON:0000468!1.62e-07!656;UBERON:0003104!5.85e-07!160;UBERON:0009142!5.85e-07!160;UBERON:0007524!7.15e-07!73;UBERON:0002199!7.69e-07!46;UBERON:0002416!7.69e-07!46
|ontology_enrichment_uberon=UBERON:0003102!5.65e-10!99;UBERON:0000479!9.76e-10!773;UBERON:0007100!1.83e-09!27;UBERON:0007023!1.01e-08!114;UBERON:0000948!5.78e-08!24;UBERON:0005498!5.78e-08!24;UBERON:0004140!5.78e-08!24;UBERON:0009881!5.78e-08!24;UBERON:0004141!5.78e-08!24;UBERON:0003084!5.78e-08!24;UBERON:0007005!5.78e-08!24;UBERON:0004139!5.78e-08!24;UBERON:0004291!5.78e-08!24;UBERON:0001013!6.18e-08!14;UBERON:0000468!1.62e-07!656;UBERON:0003104!5.85e-07!160;UBERON:0009142!5.85e-07!160;UBERON:0007524!7.15e-07!73;UBERON:0002199!7.69e-07!46;UBERON:0002416!7.69e-07!46
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2,0.229996,0.0437786,0.00127579
|tfbs_overrepresentation_for_novel_motifs=0.144412,0.000333902,0.139625,0.678862,0.364884,0.675949,0.300393,0.0518257,0.189397,0.00242338,0.218065,0.335828,0.137255,0.291158,0.112824,0.3998,0.489874,0.0827014,0.151825,0.0465461,0.431825,0.0665914,0.234854,1.18916,0.170101,0.354732,0.0273046,0.233219,0.115495,0.0226422,0.202067,0.522822,0.0662338,0.0349618,0.0937035,0.00978332,0.0919402,0.241614,0.574398,0.04349,1.57903,0.190375,0.323893,2.376,0.00338453,0.15988,0.301272,0.21008,0.292932,0.115573,0.366671,0.310813,0.0632877,0.592653,0.734926,0.293507,0.757014,0.267557,0.0979814,0.266768,0.559896,0.303183,0.0509632,0.465305,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.181085,0.0543134,0.0128276,0.73304,0.0326098,0.118275,0.104456,0.450429,0.510572,0.165891,0.647118,1.17309,1.53638,0.0530449,0.684728,0.00542149,0.045598,0.021314,0.38876,1.27332,0.90828,0.659533,1.33027,0.897208,0.114084,0.947698,0.346672,0.576706,0.392699,0.389681,0.274502,2.26929,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,0.169928,0.104263,0.146911,0.569087,0.136085,0.225069,0.862131,0.631548,0.0298336,0.201199,0.433061,0.908139,0.725237,1.00454,0.23864,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.265268,0.660176,0.204142,0.779127,4.24617,0.920697,0.0869056,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,2.40187,0.426604,0.260955,0.412168,1.56567,0.188015,0.0681329,0.0107783,0.00407349,0.660531,0.047435,0.302791,1.04704,0.374997,0.699176,0.170141,0.150717,0.842888,0.643319,0.509866,0.152845,1.96266,0.316832,0.0623453,0.299321,0.000933382
}}
}}

Revision as of 14:17, 26 November 2012


Full id: C540_tenocyte_Chondrocyte_Adipocyte_normal_Synoviocyte_Fibroblast_heart



Phase1 CAGE Peaks

Hg19::chr12:91539701..91539744,-p@chr12:91539701..91539744
-
Hg19::chr12:91539859..91539910,-p@chr12:91539859..91539910
-
Hg19::chr12:91539918..91539946,-p@chr12:91539918..91539946
-
Hg19::chr12:91545551..91545568,-p@chr12:91545551..91545568
-
Hg19::chr12:91546941..91546972,-p10@DCN
Hg19::chr12:91550883..91550925,-p@chr12:91550883..91550925
-
Hg19::chr12:91552107..91552118,-p@chr12:91552107..91552118
-
Hg19::chr12:91552211..91552251,-p@chr12:91552211..91552251
-
Hg19::chr12:91558446..91558493,-p@chr12:91558446..91558493
-
Hg19::chr12:91572143..91572274,-p6@DCN
Hg19::chr12:91572278..91572327,-p9@DCN
Hg19::chr12:91572389..91572404,-p14@DCN
Hg19::chr12:91573013..91573042,-p@chr12:91573013..91573042
-
Hg19::chr12:91573228..91573245,-p4@DCN
Hg19::chr12:91573249..91573308,-p2@DCN
Hg19::chr12:91573316..91573365,-p3@DCN
Hg19::chr6:125573037..125573043,+p@chr6:125573037..125573043
+


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
fibroblast5.69e-1776
fat cell1.67e-0915
preadipocyte5.38e-0812
skin fibroblast8.34e-0823
GAG secreting cell9.07e-079
carbohydrate secreting cell9.07e-079
Uber Anatomy
Ontology termp-valuen
surface structure5.65e-1099
tissue9.76e-10773
primary circulatory organ1.83e-0927
adult organism1.01e-08114
heart5.78e-0824
primitive heart tube5.78e-0824
primary heart field5.78e-0824
anterior lateral plate mesoderm5.78e-0824
heart tube5.78e-0824
heart primordium5.78e-0824
cardiac mesoderm5.78e-0824
cardiogenic plate5.78e-0824
heart rudiment5.78e-0824
adipose tissue6.18e-0814
multi-cellular organism1.62e-07656
mesenchyme5.85e-07160
entire embryonic mesenchyme5.85e-07160
dense mesenchyme tissue7.15e-0773
integument7.69e-0746
integumental system7.69e-0746


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)

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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.