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Coexpression cluster:C1578: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;2:11.3477820414428:0.0115705693374132:0.0422834490720493!MAFK#7975;2:10.840293255132:0.0126368327733788:0.0456844535296794!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402117771409108!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00713953037073748
|tf_chipseq_enrich=BCL11A#53335;2:11.3477820414428:0.0115705693374132:0.0422834490720493!MAFK#7975;2:10.840293255132:0.0126368327733788:0.0456844535296794!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402117771409108!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00713953037073748
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,1.56012,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.757784,0.413782,0.654459,1.00769,0.301779,1.06799,0.580638,0.132849,1.14615,0.0606304,0.533483,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.554326,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,1.57121,1.18161,0.0719601,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,1.74559,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 14:58, 26 November 2012


Full id: C1578_CD14_CD4_Basophils_Eosinophils_Neutrophils_Peripheral_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:43634422..43634481,-p@chr10:43634422..43634481
-
Hg19::chr12:90257972..90257986,+p@chr12:90257972..90257986
+
Hg19::chr12:90257987..90258016,+p@chr12:90257987..90258016
+
Hg19::chr2:235217704..235217719,+p@chr2:235217704..235217719
+
Hg19::chrX:13105644..13105658,+p@chrX:13105644..13105658
+


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
leukocyte8.62e-73136
classical monocyte1.81e-7142
CD14-positive, CD16-negative classical monocyte1.81e-7142
defensive cell7.48e-6148
phagocyte7.48e-6148
nongranular leukocyte2.09e-60115
hematopoietic lineage restricted progenitor cell1.93e-58120
myeloid leukocyte4.67e-5772
hematopoietic stem cell1.46e-56168
angioblastic mesenchymal cell1.46e-56168
hematopoietic cell1.37e-52177
hematopoietic oligopotent progenitor cell6.00e-51161
hematopoietic multipotent progenitor cell6.00e-51161
macrophage dendritic cell progenitor5.60e-4961
granulocyte monocyte progenitor cell1.03e-4767
monopoietic cell5.04e-4659
monocyte5.04e-4659
monoblast5.04e-4659
promonocyte5.04e-4659
myeloid lineage restricted progenitor cell5.89e-4466
myeloid cell2.54e-36108
common myeloid progenitor2.54e-36108
stuff accumulating cell9.53e-2887
intermediate monocyte1.95e-189
CD14-positive, CD16-positive monocyte1.95e-189
mesenchymal cell1.00e-15354
mature alpha-beta T cell2.36e-1518
alpha-beta T cell2.36e-1518
immature T cell2.36e-1518
mature T cell2.36e-1518
immature alpha-beta T cell2.36e-1518
connective tissue cell5.02e-15361
lymphoid lineage restricted progenitor cell4.03e-1352
granulocyte4.10e-138
lymphocyte9.35e-1353
common lymphoid progenitor9.35e-1353
motile cell1.40e-12386
CD4-positive, alpha-beta T cell2.44e-126
nucleate cell4.56e-1255
stem cell8.32e-11441
multi fate stem cell3.83e-10427
T cell3.92e-1025
pro-T cell3.92e-1025
somatic stem cell9.86e-10433
blood cell3.79e-0911
basophil1.01e-073
CD8-positive, alpha-beta T cell3.25e-0711
natural killer cell5.41e-073
pro-NK cell5.41e-073
single nucleate cell7.30e-073
mononuclear cell7.30e-073
naive T cell9.82e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.08e-5298
blood island9.08e-5298
hemolymphoid system2.00e-45108
bone marrow1.61e-4276
bone element2.05e-3882
immune system2.76e-3793
skeletal element8.56e-3490
skeletal system4.57e-29100
lateral plate mesoderm1.34e-16203
connective tissue4.48e-14371
musculoskeletal system2.73e-12167
blood1.33e-0815
haemolymphatic fluid1.33e-0815
organism substance1.33e-0815


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
BCL11A#53335211.34778204144280.01157056933741320.0422834490720493
MAFK#7975210.8402932551320.01263683277337880.0456844535296794
NANOG#79923211.69791139240510.01091164951956080.0402117771409108
SPI1#668846.563458806818180.0009957429636454020.00713953037073748



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.