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Coexpression cluster:C1281: Difference between revisions

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|tf_chipseq_enrich=MAFF#23764;3:24.1351527814051:0.000185591946154537:0.00224678767409686!MAFK#7975;3:11.6145999162128:0.00157162661744092:0.00996594488760853
|tf_chipseq_enrich=MAFF#23764;3:24.1351527814051:0.000185591946154537:0.00224678767409686!MAFK#7975;3:11.6145999162128:0.00157162661744092:0.00996594488760853
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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.100351,0.384703,0.529489,0.343148,1.30874,0.604235,0.643217,0.637583,0.0544999,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,1.43406,0.19568,0.66776,0.384762,0.23059,0.520063,0.897212,0.430372,0.670692,0.49486,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,0.186138,0.309012,0.71891,0.305874,0.529001,0.282922,0.207499,0.829015,0.459366,0.254304,0.340293,0.109128,0.415364,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,1.22295,0.115253,1.0929,0.179863,0.168304,2.11647,0.782748,0.850825,1.0864,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.759662,0.566252,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,1.53817,1.33983,0.783512,1.45665,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,1.18454,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,0.26104,0.106334,0.0685123,1.0153,0.619774,0.607223,1.42052,0.694887,1.57862,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
}}
}}

Revision as of 14:47, 26 November 2012


Full id: C1281_Smooth_Fibroblast_Adipocyte_Olfactory_leiomyoma_Preadipocyte_tenocyte



Phase1 CAGE Peaks

Hg19::chr7:128394431..128394448,+p@chr7:128394431..128394448
+
Hg19::chr7:128399002..128399018,+p4@CALU
Hg19::chr7:128399025..128399043,+p@chr7:128399025..128399043
+
Hg19::chr7:128399054..128399065,+p@chr7:128399054..128399065
+
Hg19::chr7:128409190..128409213,+p@chr7:128409190..128409213
+
Hg19::chr7:128409381..128409428,+p@chr7:128409381..128409428
+
Hg19::chr7:128410484..128410495,+p@chr7:128410484..128410495
+


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue4.16e-1273
somite4.59e-1271
presomitic mesoderm4.59e-1271
presumptive segmental plate4.59e-1271
dermomyotome4.59e-1271
trunk paraxial mesoderm4.59e-1271
skeletal muscle tissue1.05e-1162
striated muscle tissue1.05e-1162
myotome1.05e-1162
paraxial mesoderm1.10e-1172
presumptive paraxial mesoderm1.10e-1172
muscle tissue2.44e-1164
musculature2.44e-1164
musculature of body2.44e-1164
multilaminar epithelium2.83e-1183
epithelial vesicle5.20e-1078
artery7.38e-1042
arterial blood vessel7.38e-1042
arterial system7.38e-1042
trunk mesenchyme8.53e-10122
unilaminar epithelium1.55e-09148
mesenchyme6.46e-09160
entire embryonic mesenchyme6.46e-09160
splanchnic layer of lateral plate mesoderm9.15e-0983
integument1.12e-0846
integumental system1.12e-0846
skin of body3.99e-0841
systemic artery4.16e-0833
systemic arterial system4.16e-0833
epithelial tube open at both ends5.14e-0859
blood vessel5.14e-0859
blood vasculature5.14e-0859
vascular cord5.14e-0859
vasculature8.43e-0878
vascular system8.43e-0878
surface structure2.32e-0799
vessel2.76e-0768
Disease
Ontology termp-valuen
ovarian cancer1.17e-0814
reproductive organ cancer9.78e-0729


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
MAFF#23764324.13515278140510.0001855919461545370.00224678767409686
MAFK#7975311.61459991621280.001571626617440920.00996594488760853



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.