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Difference between revisions of "Coexpression cluster:C500"

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|tf_chipseq_enrich=CTCF#10664;10:2.82118756477633:0.00089703736288379:0.00667562242712128!POLR2A#5430;18:2.03442932516028:1.12471092130166e-05:0.000287760127167623!RFX5#5993;6:3.80460341911424:0.00343118508361132:0.0174608750644293!WRNIP1#56897;2:11.5599962473027:0.0127864612829103:0.0460103786495957
 
|tf_chipseq_enrich=CTCF#10664;10:2.82118756477633:0.00089703736288379:0.00667562242712128!POLR2A#5430;18:2.03442932516028:1.12471092130166e-05:0.000287760127167623!RFX5#5993;6:3.80460341911424:0.00343118508361132:0.0174608750644293!WRNIP1#56897;2:11.5599962473027:0.0127864612829103:0.0460103786495957
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.771519,0.0186174,0.117015,0.608931,0.643195,0.21101,0.267678,0.154541,0.15167,0.282303,0.555125,0.815436,0.0249549,0.717931,0.309279,0.343795,0.450873,0.0660543,0.11878,0.202562,0.11705,0.532315,0.592949,0.0907812,0.14499,0.3198,0.218477,0.203923,0.0951691,0.189331,0.5188,0.483059,0.192477,0.790818,0.943201,0.23618,0.547915,0.6081,2.96059,0.568676,0.552378,0.492059,1.13911,0.0919607,0.105583,0.135566,0.268517,0.53703,0.363943,0.651467,1.58554,0.760991,0.125437,1.35889,0.691633,0.261104,1.10065,0.665859,0.369868,0.235655,0.519357,0.270343,0.35087,0.426924,0.776161,0.397545,0.774525,1.12911,0.473932,0.971498,0.155159,0.0416193,0.00841861,0.689771,0.0237,0.0900341,0.0784103,0.412445,0.471083,0.141103,0.12373,1.09026,0.284019,0.361652,0.642096,0.243259,0.0310223,0.0691846,0.352635,1.2264,0.863265,0.617268,0.497892,0.775775,0.312345,0.0604965,0.521585,1.32572,0.937936,0.524507,0.228095,0.492893,0.530844,0.45406,0.387815,0.186536,0.440324,0.256236,0.444857,0.288337,0.123668,0.528368,0.113792,0.570939,0.817503,0.255662,0.000591987,0.173882,0.395564,0.451443,0.682065,0.350633,0.209033,0.292875,0.923346,0.413094,0.262802,0.502315,0.721838,0.219699,0.617901,0.176632,0.73532,0.290252,0.875585,1.18944,0.170663,0.204325,0.83506,1.67608,1.2779,0.799588,0.264127,0.532681,0.389296,0.23014,0.375295,1.51807,0.161595,0.0534036,0.225987,0.0148103,0.618251,0.0358505,0.269969,1.0011,0.339339,0.607655,0.445353,0.127152,0.798435,0.601304,0.470393,0.404939,0.402913,0.774125,0.720567,0.266654,0.31617
 
}}
 
}}

Revision as of 05:15, 26 November 2012


Full id: C500_Neutrophils_Monocytederived_blood_CD14_Eosinophils_lung_mixed



Phase1 CAGE Peaks

  Short description
Hg19::chr12:65090856..65090873,+ p@chr12:65090856..65090873
+
Hg19::chr15:45007619..45007649,+ p6@B2M
Hg19::chr15:45007659..45007713,+ p3@B2M
Hg19::chr15:45007740..45007774,+ p5@B2M
Hg19::chr15:45007776..45007836,+ p2@B2M
Hg19::chr15:45009798..45009900,+ p@chr15:45009798..45009900
+
Hg19::chr15:45009902..45010022,+ p@chr15:45009902..45010022
+
Hg19::chr1:203276836..203276855,+ p@chr1:203276836..203276855
+
Hg19::chr6:29691484..29691495,+ p3@HLA-F
Hg19::chr6:30458007..30458044,+ p@chr6:30458007..30458044
+
Hg19::chr6:30458081..30458117,+ p@chr6:30458081..30458117
+
Hg19::chr6:30458196..30458253,+ p@chr6:30458196..30458253
+
Hg19::chr6:30460680..30460737,+ +
p@chr6:30460680..30460737
Hg19::chr6:31239406..31239455,+ p@chr6:31239406..31239455
+
Hg19::chr6:31321862..31321941,- p1@X07061
p1@X07062
Hg19::chr6:31322867..31322902,+ p@chr6:31322867..31322902
+
Hg19::chr6:31322916..31322974,- p4@HLA-B
Hg19::chr6:31323216..31323285,- p3@HLA-C
p5@HLA-B
Hg19::chr6:31324641..31324664,- p10@HLA-B


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
0.0001517463875231860.008004621941848052204Endocytosis (KEGG):04144
8.87028067484744e-050.005104443333798572156Phagosome (KEGG):04145
6.73840783266509e-050.0042654121580772136Cell adhesion molecules (CAMs) (KEGG):04514
1.96249599285332e-086.21129981738076e-06378Antigen processing and presentation (KEGG):04612
7.28240379719336e-060.000768293600603899245Type I diabetes mellitus (KEGG):04940
1.05241687813521e-050.000951685548370838254Autoimmune thyroid disease (KEGG):05320
5.45153351157612e-060.000768293600603899239Allograft rejection (KEGG):05330
6.64274556874299e-060.000768293600603899243Graft-versus-host disease (KEGG):05332
1.87899740683929e-050.00132156150947697272Viral myocarditis (KEGG):05416
1.48230348787841e-050.00117287263478379264Proteasome Degradation (Wikipathways):WP183
5.70320151504265e-060.0007682936006038993511Signaling in Immune system (Reactome):REACT_6900
5.37212511845661e-093.40055519998304e-06351{HLA-A,53} (Static Module):NA



Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0002474antigen processing and presentation of peptide antigen via MHC class I3.44283425591547e-07
GO:0048002antigen processing and presentation of peptide antigen3.44283425591547e-07
GO:0042612MHC class I protein complex2.48279173867282e-06
GO:0042611MHC protein complex7.44220434057843e-06
GO:0019882antigen processing and presentation8.68789839607204e-06
GO:0032393MHC class I receptor activity1.03087902489797e-05
GO:0006955immune response0.000146634857782203
GO:0002376immune system process0.000203303733848579
GO:0044459plasma membrane part0.000810460688395914
GO:0043234protein complex0.00146544028199587
GO:0005886plasma membrane0.0029844998842909
GO:0032991macromolecular complex0.0029844998842909
GO:0004888transmembrane receptor activity0.0188521394295296
GO:0044425membrane part0.0201582891042318
GO:0004872receptor activity0.0354197492238477
GO:0016020membrane0.0354197492238477
GO:0004871signal transducer activity0.0442459626345693
GO:0060089molecular transducer activity0.0442459626345693



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
leukocyte2.94e-45136
nongranular leukocyte2.60e-40115
hematopoietic lineage restricted progenitor cell9.46e-36120
hematopoietic stem cell3.14e-31168
angioblastic mesenchymal cell3.14e-31168
hematopoietic cell4.59e-30177
hematopoietic oligopotent progenitor cell6.78e-30161
hematopoietic multipotent progenitor cell6.78e-30161
defensive cell1.44e-2848
phagocyte1.44e-2848
myeloid leukocyte1.98e-2872
macrophage dendritic cell progenitor5.28e-2761
monopoietic cell2.27e-2659
monocyte2.27e-2659
monoblast2.27e-2659
promonocyte2.27e-2659
classical monocyte2.94e-2542
CD14-positive, CD16-negative classical monocyte2.94e-2542
granulocyte monocyte progenitor cell1.35e-2367
myeloid lineage restricted progenitor cell7.00e-2266
myeloid cell1.81e-16108
common myeloid progenitor1.81e-16108
mesenchymal cell1.04e-15354
connective tissue cell5.69e-15361
multi fate stem cell3.68e-13427
lymphocyte5.11e-1353
common lymphoid progenitor5.11e-1353
lymphoid lineage restricted progenitor cell6.15e-1352
somatic stem cell1.29e-11433
nucleate cell2.36e-1155
stem cell5.67e-11441
stuff accumulating cell2.04e-0987
motile cell3.34e-09386
mature alpha-beta T cell3.46e-0918
alpha-beta T cell3.46e-0918
immature T cell3.46e-0918
mature T cell3.46e-0918
immature alpha-beta T cell3.46e-0918
T cell5.78e-0825
pro-T cell5.78e-0825
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.78e-29108
hematopoietic system6.19e-2998
blood island6.19e-2998
immune system2.32e-2293
bone marrow3.36e-2176
bone element1.21e-1782
connective tissue8.02e-15371
skeletal element1.36e-1490
lateral plate mesoderm1.31e-13203
skeletal system1.06e-12100
mesoderm6.15e-09315
mesoderm-derived structure6.15e-09315
presumptive mesoderm6.15e-09315
musculoskeletal system1.45e-08167
blood4.97e-0815
haemolymphatic fluid4.97e-0815
organism substance4.97e-0815


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
CTCF#10664102.821187564776330.000897037362883790.00667562242712128
POLR2A#5430182.034429325160281.12471092130166e-050.000287760127167623
RFX5#599363.804603419114240.003431185083611320.0174608750644293
WRNIP1#56897211.55999624730270.01278646128291030.0460103786495957



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.