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Coexpression cluster:C844: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;3:8.51083653108212:0.00435985480765636:0.0206718516482872!IRF4#3662;3:6.57435380602324:0.00894914180685731:0.0339375243706017!NFKB1#4790;6:3.2928380545163:0.0039127525205927:0.0190705600381828
|tf_chipseq_enrich=BCL11A#53335;3:8.51083653108212:0.00435985480765636:0.0206718516482872!IRF4#3662;3:6.57435380602324:0.00894914180685731:0.0339375243706017!NFKB1#4790;6:3.2928380545163:0.0039127525205927:0.0190705600381828
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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.383295,0.273994,0.404877,0.237701,0.403356,0.474413,0.140612,0.847231,0.230076,0.375531,0.515448,0.107365,0.46359,0.236531,0.256724,0.68716,0.191625,0.116269,0.400542,0.274046,0.111654,1.02534,0.658697,0.314616,1.32829,0.310025,0.39419,0.675066,0.590419,0.935963,0.722879,0.495657,0.108961,0.20845,1.47818,0.593726,0.404426,0.547451,1.28559,0.597291,0.340749,0.554904,0.235234,0.644296,0.301189,0.47544,0.365597,0.827284,0.240465,0.550604,0.486559,0.214602,0.797754,0.947672,0.466348,0.244111,0.435652,0.281305,0.434711,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.144996,0.0579262,0.945703,0.104203,0.652929,0.0867529,1.55336,0.709631,0.309107,0.380738,0.659298,0.49429,0.439665,0.89511,0.0510741,2.03773,0.971783,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,1.02531,0.115206,0.780743,0.579925,1.86935,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.7752,0.772599,0.741574,0.384185,1.07963,0.204477,0.0648813,0.354459,0.624851,0.991665,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,1.25332,1.13991,0.0752959,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,1.82998,0.617705,0.42776,0.601672,1.79367,0.896414,0.168379,0.193209,0.0287097,0.869654,0.821366,0.477214,1.26919,1.37691,0.225815,0.844822,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.479645,0.473159,0.0683071
}}
}}

Revision as of 14:30, 26 November 2012


Full id: C844_Mast_CD14_immature_Eosinophils_carcinoid_Natural_CD34



Phase1 CAGE Peaks

Hg19::chr17:7747614..7747633,+p@chr17:7747614..7747633
+
Hg19::chr17:7749921..7749951,+p@chr17:7749921..7749951
+
Hg19::chr1:155947466..155947477,-p@chr1:155947466..155947477
-
Hg19::chr1:155947503..155947518,-p@chr1:155947503..155947518
-
Hg19::chr1:224022601..224022610,-p@chr1:224022601..224022610
-
Hg19::chr2:201997565..201997576,+p42@CFLAR
Hg19::chr4:164087974..164088088,-p1@NAF1
Hg19::chr7:106810484..106810494,+p4@HBP1
Hg19::chr9:102590331..102590358,+p1@AB384783
Hg19::chrX:45613380..45613402,-p@chrX:45613380..45613402
-


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


GO IDGO nameFDR corrected p-value
GO:0048523negative regulation of cellular process0.0489883656349895
GO:0048519negative regulation of biological process0.0489883656349895



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
leukocyte4.18e-45136
classical monocyte2.50e-4142
CD14-positive, CD16-negative classical monocyte2.50e-4142
myeloid leukocyte2.46e-3672
hematopoietic lineage restricted progenitor cell3.37e-36120
defensive cell1.52e-3448
phagocyte1.52e-3448
granulocyte monocyte progenitor cell2.04e-3467
hematopoietic cell7.96e-34177
nongranular leukocyte1.63e-33115
hematopoietic stem cell4.39e-33168
angioblastic mesenchymal cell4.39e-33168
hematopoietic oligopotent progenitor cell1.11e-31161
hematopoietic multipotent progenitor cell1.11e-31161
myeloid lineage restricted progenitor cell3.57e-3166
macrophage dendritic cell progenitor8.14e-3161
monopoietic cell2.63e-2859
monocyte2.63e-2859
monoblast2.63e-2859
promonocyte2.63e-2859
myeloid cell4.04e-26108
common myeloid progenitor4.04e-26108
stuff accumulating cell7.65e-1887
mesenchymal cell5.71e-10354
connective tissue cell2.33e-09361
circulating cell2.79e-096
Langerhans cell1.65e-075
motile cell2.84e-07386
conventional dendritic cell3.95e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.81e-3298
blood island4.81e-3298
hemolymphoid system1.09e-28108
bone marrow1.28e-2876
bone element2.99e-2882
immune system7.40e-2793
skeletal element2.02e-2490
skeletal system1.59e-20100
lateral plate mesoderm4.58e-10203
connective tissue5.33e-09371
musculoskeletal system1.38e-08167


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


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

TF#promotersEnrichmentp-valueq-value
BCL11A#5333538.510836531082120.004359854807656360.0206718516482872
IRF4#366236.574353806023240.008949141806857310.0339375243706017
NFKB1#479063.29283805451630.00391275252059270.0190705600381828



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.