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Difference between revisions of "Coexpression cluster:C870"

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|ontology_enrichment_uberon=UBERON:0002390!6.69e-23!98;UBERON:0003061!6.69e-23!98;UBERON:0002193!1.18e-20!108;UBERON:0002371!3.85e-18!76;UBERON:0001474!9.82e-17!82;UBERON:0004765!3.80e-15!90;UBERON:0002405!1.28e-14!93;UBERON:0001434!1.64e-13!100;UBERON:0003081!3.10e-10!203;UBERON:0000178!4.43e-08!15;UBERON:0000179!4.43e-08!15;UBERON:0000463!4.43e-08!15;UBERON:0002204!1.47e-07!167;UBERON:0002384!9.92e-07!371
 
|ontology_enrichment_uberon=UBERON:0002390!6.69e-23!98;UBERON:0003061!6.69e-23!98;UBERON:0002193!1.18e-20!108;UBERON:0002371!3.85e-18!76;UBERON:0001474!9.82e-17!82;UBERON:0004765!3.80e-15!90;UBERON:0002405!1.28e-14!93;UBERON:0001434!1.64e-13!100;UBERON:0003081!3.10e-10!203;UBERON:0000178!4.43e-08!15;UBERON:0000179!4.43e-08!15;UBERON:0000463!4.43e-08!15;UBERON:0002204!1.47e-07!167;UBERON:0002384!9.92e-07!371
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.83884,0.479568,0.305225,0.440628,0.737182,0.439064,0.511871,0.164003,0.487494,0.119197,0.410439,0.553754,0.40163,0.500805,0.266007,0.287179,0.728104,0.218596,0.426514,0.0599474,0.305279,0.141777,0.431698,0.726652,0.347482,0.575764,0.36063,0.429643,0.74357,0.10044,0.389837,0.764231,0.557092,0.406122,0.23642,0.261421,0.233607,0.440165,0.213144,0.14756,0.663028,0.374544,0.366128,0.264644,0.149259,0.887061,0.51292,0.4002,0.147122,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.253077,0.988898,1.27856,0.114787,0.342172,0.684401,0.750836,0.341765,0.141333,0.699894,0.532172,0.166331,0.937974,0.358653,0.214403,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,1.08517,0.267904,0.207949,0.423564,0.82268,1.50181,0.0858425,0.613956,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,1.24409,0.347247,0.704291,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.685543,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.565137,0.50389,0.347165,0.912334,0.155464,1.28086,1.31376,0.599133,0.708413,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,1.61842
 
}}
 
}}

Revision as of 05:31, 26 November 2012


Full id: C870_CD14_Mast_Basophils_Peripheral_Eosinophils_Endothelial_Natural



Phase1 CAGE Peaks

Hg19::chr10:17010725..17010731,-p@chr10:17010725..17010731
-
Hg19::chr11:93256270..93256311,+p@chr11:93256270..93256311
+
Hg19::chr19:13953553..13953571,+p@chr19:13953553..13953571
+
Hg19::chr4:139937826..139937827,+p@chr4:139937826..139937827
+
Hg19::chr4:140656102..140656142,-p@chr4:140656102..140656142
-
Hg19::chr4:140657557..140657602,-p@chr4:140657557..140657602
-
Hg19::chr4:40058783..40058795,-p3@LOC344967
Hg19::chr5:172194496..172194500,-p@chr5:172194496..172194500
-
Hg19::chr6:138192305..138192312,+p51@TNFAIP3


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:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0102437301306959



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
single nucleate cell6.54e-383
mononuclear cell6.54e-383
classical monocyte2.70e-3442
CD14-positive, CD16-negative classical monocyte2.70e-3442
defensive cell7.35e-3048
phagocyte7.35e-3048
monopoietic cell1.21e-2359
monocyte1.21e-2359
monoblast1.21e-2359
promonocyte1.21e-2359
myeloid leukocyte5.28e-2372
macrophage dendritic cell progenitor7.71e-2361
nongranular leukocyte2.27e-22115
leukocyte1.69e-21136
myeloid lineage restricted progenitor cell4.85e-2166
granulocyte monocyte progenitor cell1.03e-2067
circulating cell2.49e-196
hematopoietic stem cell4.19e-17168
angioblastic mesenchymal cell4.19e-17168
hematopoietic cell3.76e-16177
stuff accumulating cell6.64e-1687
myeloid cell6.27e-15108
common myeloid progenitor6.27e-15108
intermediate monocyte2.09e-139
CD14-positive, CD16-positive monocyte2.09e-139
hematopoietic lineage restricted progenitor cell2.74e-13120
hematopoietic oligopotent progenitor cell2.30e-11161
hematopoietic multipotent progenitor cell2.30e-11161
mesenchymal cell3.77e-07354
connective tissue cell5.67e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.69e-2398
blood island6.69e-2398
hemolymphoid system1.18e-20108
bone marrow3.85e-1876
bone element9.82e-1782
skeletal element3.80e-1590
immune system1.28e-1493
skeletal system1.64e-13100
lateral plate mesoderm3.10e-10203
blood4.43e-0815
haemolymphatic fluid4.43e-0815
organism substance4.43e-0815
musculoskeletal system1.47e-07167
connective tissue9.92e-07371


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.