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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:42, 17 September 2013


Full id: C1311_Neutrophils_Whole_Eosinophils_Basophils_blood_CD4_CD14



Phase1 CAGE Peaks

Hg19::chr10:31876301..31876306,-p@chr10:31876301..31876306
-
Hg19::chr15:58443521..58443530,+p7@ENST00000559334
Hg19::chr3:46283839..46283854,+p4@CCR3
Hg19::chr3:46283863..46283874,+p6@CCR3
Hg19::chr3:46283880..46283890,+p7@CCR3
Hg19::chr3:46283916..46283927,+p2@CCR3


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:0016493C-C chemokine receptor activity0.0136919479907823
GO:0019957C-C chemokine binding0.0136919479907823
GO:0001637G-protein chemoattractant receptor activity0.0136919479907823
GO:0004950chemokine receptor activity0.0136919479907823
GO:0019956chemokine binding0.0136919479907823
GO:0051480cytosolic calcium ion homeostasis0.0136919479907823
GO:0007204elevation of cytosolic calcium ion concentration0.0136919479907823
GO:0006968cellular defense response0.0136919479907823
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0136919479907823
GO:0019933cAMP-mediated signaling0.0136919479907823
GO:0019955cytokine binding0.0136919479907823
GO:0055074calcium ion homeostasis0.0136919479907823
GO:0006874cellular calcium ion homeostasis0.0136919479907823
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0136919479907823
GO:0019935cyclic-nucleotide-mediated signaling0.0136919479907823
GO:0006875cellular metal ion homeostasis0.0136919479907823
GO:0055065metal ion homeostasis0.0136919479907823
GO:0042330taxis0.0136919479907823
GO:0006935chemotaxis0.0136919479907823
GO:0001653peptide receptor activity0.0136919479907823
GO:0008528peptide receptor activity, G-protein coupled0.0136919479907823
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0148136700812434
GO:0007626locomotory behavior0.0148136700812434
GO:0055066di-, tri-valent inorganic cation homeostasis0.0148136700812434
GO:0030003cellular cation homeostasis0.014966573779714
GO:0055080cation homeostasis0.014966573779714
GO:0042277peptide binding0.014966573779714
GO:0055082cellular chemical homeostasis0.0158771726817623
GO:0006873cellular ion homeostasis0.0158771726817623
GO:0050801ion homeostasis0.0167956153644557
GO:0019932second-messenger-mediated signaling0.0167956153644557
GO:0006954inflammatory response0.0172564257069836
GO:0007610behavior0.0172564257069836
GO:0048878chemical homeostasis0.0172564257069836
GO:0019725cellular homeostasis0.0208154614724731
GO:0009611response to wounding0.0228276227481455
GO:0042592homeostatic process0.0252035857828864
GO:0006952defense response0.0293409051798313
GO:0042221response to chemical stimulus0.0293409051798313
GO:0009605response to external stimulus0.0307444365948428
GO:0065008regulation of biological quality0.0433736127426417
GO:0022610biological adhesion0.0433736127426417
GO:0007155cell adhesion0.0433736127426417



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
myeloid leukocyte4.80e-2572
classical monocyte1.70e-2142
CD14-positive, CD16-negative classical monocyte1.70e-2142
granulocyte7.66e-208
defensive cell2.40e-1848
phagocyte2.40e-1848
myeloid cell1.77e-16108
common myeloid progenitor1.77e-16108
monopoietic cell6.53e-1659
monocyte6.53e-1659
monoblast6.53e-1659
promonocyte6.53e-1659
leukocyte6.53e-16136
myeloid lineage restricted progenitor cell1.14e-1566
macrophage dendritic cell progenitor2.84e-1561
neutrophil2.21e-143
blood cell3.02e-1411
granulocyte monocyte progenitor cell1.39e-1367
hematopoietic stem cell7.93e-13168
angioblastic mesenchymal cell7.93e-13168
hematopoietic cell7.43e-12177
hematopoietic oligopotent progenitor cell2.38e-11161
hematopoietic multipotent progenitor cell2.38e-11161
nongranular leukocyte1.13e-10115
eosinophil4.66e-102
hematopoietic lineage restricted progenitor cell6.53e-09120
stuff accumulating cell1.56e-0887
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.82e-2998
blood island4.82e-2998
blood5.60e-2815
haemolymphatic fluid5.60e-2815
organism substance5.60e-2815
hemolymphoid system9.56e-26108
bone marrow1.50e-1176
immune system2.83e-1193
lateral plate mesoderm1.28e-10203
bone element1.92e-1082
skeletal element3.37e-0990
skeletal system6.26e-08100


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.13.34657
MA0038.11.59836
MA0040.12.19519
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.12.90543
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.16.95755
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.12.3765
MA0084.13.39228
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.419295
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.12.77189
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.12.56485
MA0154.10.132326
MA0155.10.0961854
MA0156.11.88357
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
MA0442.10



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
PBX3#5090414.60967512449616.03404227507469e-050.000991019564658792
SPI1#668845.469549005681820.00269730053614140.0148389891853177



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.

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