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Coexpression cluster:C1215: Difference between revisions

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|tf_chipseq_enrich=NFKB1#4790;6:4.70405436359472:0.00021611506140197:0.00247758956067622!POU2F2#5452;5:6.50437432695895:0.000276785134033055:0.00294850699849839!RFX5#5993;5:8.60565059085364:7.16524263203101e-05:0.00112751359838283!SRF#6722;3:5.91307639807192:0.0106686813016745:0.0393956230408933
|tf_chipseq_enrich=NFKB1#4790;6:4.70405436359472:0.00021611506140197:0.00247758956067622!POU2F2#5452;5:6.50437432695895:0.000276785134033055:0.00294850699849839!RFX5#5993;5:8.60565059085364:7.16524263203101e-05:0.00112751359838283!SRF#6722;3:5.91307639807192:0.0106686813016745:0.0393956230408933
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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.637583,0.200685,0.497563,0.647852,0.184039,0.592674,0.341795,0.956905,0.827563,0.786991,0.569568,0.0986842,0.384762,0.85713,0.520063,0.338096,0.430372,0.670692,0.49486,0.517892,0.346214,0.459534,0.475674,0.864517,1.31702,0.546594,0.309012,0.232776,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,0.902101,0.494995,0.415364,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.897759,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,0.115253,1.0929,0.179863,0.168304,0.921933,0.782748,0.850825,3.87752,1.099,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.88003,0.711163,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,1.41651,0.875714,2.11992,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.821533,0.642446,1.19482,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.433733,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,0.456039,0.26104,0.345641,0.0685123,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.033943
}}
}}

Revision as of 14:45, 26 November 2012


Full id: C1215_migratory_CD19_adult_immature_Dendritic_Burkitt_vein



Phase1 CAGE Peaks

Hg19::chr16:10972516..10972521,+p@chr16:10972516..10972521
+
Hg19::chr1:151319654..151319698,-p2@RFX5
Hg19::chr6:150954152..150954194,+p@chr6:150954152..150954194
+
Hg19::chr6:32977327..32977330,-p3@HLA-DOA
Hg19::chr6:32977332..32977343,-p2@HLA-DOA
Hg19::chr6:32977345..32977394,-p1@HLA-DOA
Hg19::chr6:33080222..33080247,+p1@HLA-DPB2


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


p.valueFDRnGenesnPathwayName
2.20729154564608e-050.0139721554839397278Antigen processing and presentation (KEGG):04612
0.0001207720034001940.03822433907616132182Tuberculosis (KEGG):05152



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:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II0.00128981675613196
GO:0042613MHC class II protein complex0.00128981675613196
GO:0042611MHC protein complex0.00609127997386628
GO:0019882antigen processing and presentation0.00609127997386628
GO:0032395MHC class II receptor activity0.0174762390536148
GO:0006955immune response0.0328749366611706
GO:0002376immune system process0.0381426036666276



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>


Cell Type
Ontology termp-valuen
leukocyte1.17e-56136
nongranular leukocyte6.80e-53115
hematopoietic lineage restricted progenitor cell3.23e-46120
hematopoietic cell4.08e-44177
hematopoietic stem cell1.08e-43168
angioblastic mesenchymal cell1.08e-43168
hematopoietic oligopotent progenitor cell1.11e-38161
hematopoietic multipotent progenitor cell1.11e-38161
lymphocyte1.63e-3253
common lymphoid progenitor1.63e-3253
lymphoid lineage restricted progenitor cell2.31e-3152
nucleate cell8.92e-3155
lymphocyte of B lineage1.03e-2824
pro-B cell1.03e-2824
B cell8.93e-2014
macrophage dendritic cell progenitor2.17e-1961
monopoietic cell1.31e-1759
monocyte1.31e-1759
monoblast1.31e-1759
promonocyte1.31e-1759
classical monocyte9.04e-1742
CD14-positive, CD16-negative classical monocyte9.04e-1742
granulocyte monocyte progenitor cell1.41e-1667
defensive cell6.13e-1648
phagocyte6.13e-1648
myeloid leukocyte1.77e-1572
myeloid lineage restricted progenitor cell1.47e-1466
dendritic cell1.80e-1410
conventional dendritic cell3.63e-128
myeloid cell9.26e-12108
common myeloid progenitor9.26e-12108
circulating cell1.32e-086
immature conventional dendritic cell4.04e-085
common dendritic progenitor4.04e-085
Langerhans cell5.28e-085
T cell4.65e-0725
pro-T cell4.65e-0725
mesenchymal cell5.15e-07354
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.15e-2798
blood island2.15e-2798
hemolymphoid system1.10e-25108
immune system3.82e-1793
bone marrow3.62e-1476
bone element2.76e-1282
blood1.94e-1115
haemolymphatic fluid1.94e-1115
organism substance1.94e-1115
skeletal element3.29e-1090
adult organism4.27e-10114
skeletal system1.01e-08100
hemopoietic organ4.34e-077
immune organ4.34e-077
Disease
Ontology termp-valuen
lymphoma1.18e-0810


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
NFKB1#479064.704054363594720.000216115061401970.00247758956067622
POU2F2#545256.504374326958950.0002767851340330550.00294850699849839
RFX5#599358.605650590853647.16524263203101e-050.00112751359838283
SRF#672235.913076398071920.01066868130167450.0393956230408933



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.