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Difference between revisions of "Coexpression cluster:C498"

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Latest revision as of 02:24, 17 September 2013


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)
MA0003.14.00557
MA0004.11.07203
MA0006.11.06559
MA0007.10.532323
MA0009.10.580032
MA0014.13.70907
MA0017.10.114723
MA0019.10.824541
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.332468
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.11.36368
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.465769
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.194883
MA0056.10
MA0057.10.254333
MA0058.11.31411
MA0059.10.405044
MA0060.10.0387582
MA0061.11.66887
MA0063.10
MA0066.10.743889
MA0067.10.879057
MA0068.10.994655
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.11.26093
MA0074.10.265952
MA0076.10.432406
MA0077.10.545231
MA0078.10.346453
MA0081.10.405301
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.126597
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.168981
MA0093.11.59065
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.654976
MA0103.10.614572
MA0105.11.96347
MA0106.10.302526
MA0107.11.2344
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.456488
MA0115.10.805883
MA0116.10.477333
MA0117.10.614633
MA0119.10.762609
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.11.69199
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.792683
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.0508083
MA0145.11.59211
MA0146.10.959919
MA0147.10.223797
MA0148.10.211171
MA0149.10.230803
MA0062.20.826291
MA0035.20.668495
MA0039.21.8612
MA0138.20.918057
MA0002.20.589508
MA0137.20.105044
MA0104.20.627988
MA0047.20.292798
MA0112.20.256517
MA0065.20.156004
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.38017
MA0155.11.44005
MA0156.10.106343
MA0157.10.384449
MA0158.10
MA0159.11.77332
MA0160.10.222325
MA0161.10
MA0162.13.71699
MA0163.11.69905
MA0164.10.32594
MA0080.21.07751
MA0018.20.30364
MA0099.20.243305
MA0079.22.84757
MA0102.21.09681
MA0258.10.177641
MA0259.10.50664
MA0442.10



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.