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Difference between revisions of "Coexpression cluster:C498"

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|tf_chipseq_enrich=BCL11A#53335;4:5.97251686391728:0.00390839570699839:0.0190502141803894!E2F1#1869;10:2.58283642888386:0.00183346537983127:0.0108527142827136!EGR1#1958;12:3.15042890198535:5.09805837530452e-05:0.000868432749402102!PAX5#5079;10:3.51029764798833:0.000142832248088682:0.00185977523477545!POLR2A#5430;18:2.03442932516028:1.12471092130166e-05:0.00028768964954647!TCF12#6938;6:3.35825207437466:0.00637219882280837:0.0277444479449403!ZEB1#6935;6:5.33318905817174:0.00059641743437254:0.00499152499626842
 
|tf_chipseq_enrich=BCL11A#53335;4:5.97251686391728:0.00390839570699839:0.0190502141803894!E2F1#1869;10:2.58283642888386:0.00183346537983127:0.0108527142827136!EGR1#1958;12:3.15042890198535:5.09805837530452e-05:0.000868432749402102!PAX5#5079;10:3.51029764798833:0.000142832248088682:0.00185977523477545!POLR2A#5430;18:2.03442932516028:1.12471092130166e-05:0.00028768964954647!TCF12#6938;6:3.35825207437466:0.00637219882280837:0.0277444479449403!ZEB1#6935;6:5.33318905817174:0.00059641743437254:0.00499152499626842
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.38505,0.544855,0.373702,0.212191,0.311264,0.21101,1.35575,0.154541,0.15167,0.639687,0.189673,0.301621,0.485349,0.258863,0.0927703,0.105638,0.450873,0.0660543,0.11878,0.572791,0.752144,1.32537,0.205464,1.05327,0.44526,0.3198,0.218477,0.203923,0.315774,0.61444,0.174693,0.483059,0.0517705,0.263718,2.54786,0.503,1.92887,0.211841,0.490545,0.897971,0.552378,0.952768,0.243154,0.0919607,0.5983,0.135566,0.74012,0.53703,0.0472843,0.315962,0.882073,0.27764,0.695308,0.551494,0.691633,0.261104,0.322175,0.665859,0.613944,1.9191,0.519357,0.744306,0.35087,1.09226,0.284296,0.397545,0.774525,1.12911,0.473932,0.971498,0.470686,0.0416193,1.69907,0.689771,1.11044,0.225538,0.0784103,0.412445,0.471083,0.141103,0.861035,0.426001,0.284019,0.157796,0.642096,2.5355,0.199201,0.0691846,0.929503,1.2264,2.00675,0.617268,0.497892,0.775775,0.0939013,0.0604965,0.521585,0.535841,0.937936,0.524507,0.0637978,0.492893,0.530844,0.45406,0.387815,0.186536,0.440324,1.31333,0.14483,0.288337,0.390957,0.528368,0.737452,1.08365,0.817503,0.0734112,3.74207,0.173882,0.395564,0.786082,0.682065,0.925065,0.209033,0.292875,0.923346,0.413094,0.262802,0.502315,0.721838,0.219699,0.617901,0.176632,0.73532,0.290252,0.875585,0.335759,0.508946,0.204325,0.83506,1.67608,1.2779,0.799588,0.264127,0.532681,0.389296,0.23014,1.73951,1.51807,0.161595,1.16815,1.22018,0.566686,0.618251,0.142739,0.269969,1.0011,0.339339,0.0861459,0.145027,0.127152,0.798435,0.601304,0.470393,0.404939,0.402913,0.774125,0.4086,2.08083,1.83601
 
}}
 
}}

Revision as of 05:15, 26 November 2012


Full id: C498_Eosinophils_Neutrophils_CD19_Burkitt_diffuse_lymphoma_CD14



Phase1 CAGE Peaks

  Short description
Hg19::chr12:40618919..40618928,+ p9@LRRK2
Hg19::chr13:46960645..46960658,- -
p@chr13:46960645..46960658
Hg19::chr13:46961337..46961359,- p2@KIAA0226L
Hg19::chr13:46961366..46961394,- p1@KIAA0226L
Hg19::chr13:46961530..46961558,- p6@KIAA0226L
Hg19::chr13:46961580..46961620,- p4@KIAA0226L
Hg19::chr13:46961859..46961883,- p5@KIAA0226L
Hg19::chr14:69152139..69152172,- p1@ENST00000556919
Hg19::chr14:69152180..69152191,- p3@ENST00000556919
Hg19::chr16:27325202..27325307,+ p1@IL4R
Hg19::chr16:81772633..81772676,+ p1@uc002fgs.2
Hg19::chr16:81812884..81812907,+ p1@PLCG2
Hg19::chr16:81812917..81812933,+ p2@PLCG2
Hg19::chr1:226862756..226862831,- p1@ITPKB-IT1
Hg19::chr1:244212954..244212968,- p@chr1:244212954..244212968
-
Hg19::chr2:69001969..69001981,+ p8@ARHGAP25
Hg19::chr3:151923200..151923235,- p@chr3:151923200..151923235
-
Hg19::chr5:56111170..56111185,+ p9@MAP3K1
Hg19::chr5:56111207..56111219,+ p3@MAP3K1


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


No results for this coexpression

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:0005057receptor signaling protein activity0.00883028193442909
GO:0004913interleukin-4 receptor activity0.00883028193442909
GO:0019979interleukin-4 binding0.00883028193442909
GO:0005096GTPase activator activity0.0230670501762326
GO:0008047enzyme activator activity0.0313681190628453
GO:0007165signal transduction0.0340275895393832
GO:0004709MAP kinase kinase kinase activity0.0340275895393832
GO:0007154cell communication0.0350460138096726
GO:0004674protein serine/threonine kinase activity0.0366141190724578
GO:0030695GTPase regulator activity0.0366141190724578
GO:0004907interleukin receptor activity0.0408633383501864
GO:0019965interleukin binding0.0424669262345909
GO:0004435phosphoinositide phospholipase C activity0.0424669262345909
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0424669262345909
GO:0004629phospholipase C activity0.0483525701900892
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0483525701900892
GO:0004672protein kinase activity0.0483525701900892
GO:0060089molecular transducer activity0.0483525701900892
GO:0004871signal transducer activity0.0483525701900892
GO:0006468protein amino acid phosphorylation0.0483525701900892
GO:0004702receptor signaling protein serine/threonine kinase activity0.0483525701900892



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
leukocyte5.54e-67136
nongranular leukocyte2.62e-58115
hematopoietic lineage restricted progenitor cell5.29e-52120
hematopoietic stem cell6.60e-52168
angioblastic mesenchymal cell6.60e-52168
myeloid leukocyte2.03e-4872
hematopoietic cell1.42e-47177
hematopoietic oligopotent progenitor cell1.47e-46161
hematopoietic multipotent progenitor cell1.47e-46161
classical monocyte3.36e-4542
CD14-positive, CD16-negative classical monocyte3.36e-4542
defensive cell2.49e-4348
phagocyte2.49e-4348
monopoietic cell5.94e-4059
monocyte5.94e-4059
monoblast5.94e-4059
promonocyte5.94e-4059
macrophage dendritic cell progenitor6.93e-4061
granulocyte monocyte progenitor cell7.89e-3867
myeloid lineage restricted progenitor cell5.87e-3766
myeloid cell6.76e-29108
common myeloid progenitor6.76e-29108
lymphocyte of B lineage1.34e-2024
pro-B cell1.34e-2024
B cell2.85e-1814
stuff accumulating cell7.63e-1787
lymphocyte1.25e-1553
common lymphoid progenitor1.25e-1553
lymphoid lineage restricted progenitor cell8.20e-1552
nucleate cell1.10e-1455
granulocyte1.33e-118
intermediate monocyte4.83e-119
CD14-positive, CD16-positive monocyte4.83e-119
mesenchymal cell5.11e-09354
connective tissue cell2.26e-08361
blood cell8.16e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.61e-4798
blood island6.61e-4798
hemolymphoid system1.83e-43108
bone marrow1.20e-3276
immune system1.49e-3293
bone element6.24e-2982
skeletal element8.87e-2590
skeletal system1.62e-21100
adult organism2.25e-17114
lateral plate mesoderm1.19e-14203
blood3.72e-1215
haemolymphatic fluid3.72e-1215
organism substance3.72e-1215
connective tissue7.51e-08371
musculoskeletal system3.48e-07167


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
BCL11A#5333545.972516863917280.003908395706998390.0190502141803894
E2F1#1869102.582836428883860.001833465379831270.0108527142827136
EGR1#1958123.150428901985355.09805837530452e-050.000868432749402102
PAX5#5079103.510297647988330.0001428322480886820.00185977523477545
POLR2A#5430182.034429325160281.12471092130166e-050.00028768964954647
TCF12#693863.358252074374660.006372198822808370.0277444479449403
ZEB1#693565.333189058171740.000596417434372540.00499152499626842



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.