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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0.

Latest revision as of 11:59, 17 September 2013


Full id: C2117_immature_CD14_Basophils_Peripheral_Neutrophils_Mast_CD19



Phase1 CAGE Peaks

Hg19::chr11:18656354..18656376,-p4@SPTY2D1
Hg19::chr13:41593392..41593403,-p7@ELF1
Hg19::chr13:41593405..41593416,-p9@ELF1
Hg19::chr3:41279208..41279212,+p@chr3:41279208..41279212
+


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:0050858negative regulation of antigen receptor-mediated signaling pathway0.00304662663369834
GO:0050860negative regulation of T cell receptor signaling pathway0.00304662663369834
GO:0050856regulation of T cell receptor signaling pathway0.00406216884493112
GO:0050854regulation of antigen receptor-mediated signaling pathway0.0050777110561639
GO:0050852T cell receptor signaling pathway0.00670257859413634
GO:0050851antigen receptor-mediated signaling pathway0.00670257859413634
GO:0002429immune response-activating cell surface receptor signaling pathway0.00670257859413634
GO:0002768immune response-regulating cell surface receptor signaling pathway0.00670257859413634
GO:0002757immune response-activating signal transduction0.00670257859413634
GO:0002764immune response-regulating signal transduction0.00670257859413634
GO:0001817regulation of cytokine production0.00757040557464436
GO:0002253activation of immune response0.0120172494995879
GO:0050778positive regulation of immune response0.0124766614522884
GO:0002684positive regulation of immune system process0.0124766614522884
GO:0050776regulation of immune response0.0125449331975814
GO:0002682regulation of immune system process0.0125449331975814
GO:0051240positive regulation of multicellular organismal process0.0125449331975814
GO:0001816cytokine production0.0127506966521449
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0148589860380375
GO:0016564transcription repressor activity0.0215681822004676
GO:0045893positive regulation of transcription, DNA-dependent0.0215681822004676
GO:0051239regulation of multicellular organismal process0.0244576415871894
GO:0045941positive regulation of transcription0.0244576415871894
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0244576415871894
GO:0016563transcription activator activity0.0251042034616743
GO:0031325positive regulation of cellular metabolic process0.0285133005461511
GO:0009893positive regulation of metabolic process0.0294131114512605
GO:0006357regulation of transcription from RNA polymerase II promoter0.0306838825251047
GO:0006366transcription from RNA polymerase II promoter0.0448239320819985



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
hematopoietic stem cell1.52e-64168
angioblastic mesenchymal cell1.52e-64168
hematopoietic oligopotent progenitor cell9.19e-62161
hematopoietic multipotent progenitor cell9.19e-62161
hematopoietic cell4.18e-60177
leukocyte6.01e-58136
hematopoietic lineage restricted progenitor cell3.33e-48120
nongranular leukocyte2.00e-46115
myeloid cell2.15e-46108
common myeloid progenitor2.15e-46108
myeloid leukocyte9.73e-4072
granulocyte monocyte progenitor cell2.67e-3567
myeloid lineage restricted progenitor cell7.88e-3466
macrophage dendritic cell progenitor2.76e-3361
monopoietic cell6.76e-3259
monocyte6.76e-3259
monoblast6.76e-3259
promonocyte6.76e-3259
defensive cell1.89e-2848
phagocyte1.89e-2848
classical monocyte3.47e-2842
CD14-positive, CD16-negative classical monocyte3.47e-2842
mesenchymal cell1.64e-14354
lymphocyte2.50e-1353
common lymphoid progenitor2.50e-1353
lymphoid lineage restricted progenitor cell3.24e-1352
nucleate cell5.31e-1355
connective tissue cell1.56e-12361
motile cell1.90e-11386
stuff accumulating cell2.11e-1187
lymphocyte of B lineage1.30e-0724
pro-B cell1.30e-0724
intermediate monocyte3.90e-079
CD14-positive, CD16-positive monocyte3.90e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.40e-3598
blood island4.40e-3598
hemolymphoid system2.42e-30108
bone marrow3.02e-3076
bone element1.02e-2882
immune system7.36e-2793
skeletal element4.48e-2490
skeletal system3.20e-19100
connective tissue4.77e-12371
Disease
Ontology termp-valuen
hematologic cancer3.98e-1051
immune system cancer3.98e-1051
leukemia2.58e-0839
myeloid leukemia9.15e-0831


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.12.91216
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.12.94475
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.20.0021048
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
BATF#10538212.17890089615180.009566758805047810.0360103338441717
BCL11A#53335214.18472755180350.007108328585298740.0296113728658615
BCLAF1#9774210.82632380506090.01202203816432580.0436385946004456
FOSL1#8061219.85678985818650.003677050009233230.0185556351910664
IRF4#3662210.95725634337210.01174530180688030.0428096452644928
JUNB#3726215.30531632991060.006126947148475620.0270922661094731
JUND#372735.245997956403270.01043432751748420.0386642090331216
MAX#414934.839416631755340.01315737137836840.0465905848438806
MEF2C#4208220.6556772463120.003402570579445040.0173541567977077
USF1#739134.771124457905970.01370465887188020.0482699604721534



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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