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{{Coexpression_clusters
{
|full_id=C4591_Neutrophils_Basophils_Eosinophils_migratory_CD14_CD4_CD8
|gostat_on_coexpression_clusters

Latest revision as of 14:15, 17 September 2013


Full id: C4591_Neutrophils_Basophils_Eosinophils_migratory_CD14_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr6:31239114..31239134,-p6@HLA-C
Hg19::chr6:31239852..31239876,-p1@HLA-C
Hg19::chr6:31324943..31324963,-p1@HLA-B


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

p.valueFDRnGenesnPathwayName
5.08218999092061e-050.002680855220210622204Endocytosis (KEGG):04144
2.96743344876993e-050.001707623066428512156Phagosome (KEGG):04145
2.25318768070372e-050.001447397695246722136Cell adhesion molecules (CAMs) (KEGG):04514
7.37072179210596e-060.000583208361800384278Antigen processing and presentation (KEGG):04612
2.28656823893637e-050.001447397695246722137Natural killer cell mediated cytotoxicity (KEGG):04650
2.42990828311186e-060.00044465996176429245Type I diabetes mellitus (KEGG):04940
3.51232197286169e-060.00044465996176429254Autoimmune thyroid disease (KEGG):05320
1.81874953311705e-060.00044465996176429239Allograft rejection (KEGG):05330
2.21637088853536e-060.00044465996176429243Graft-versus-host disease (KEGG):05332
6.2735813854888e-060.00056731100243063272Viral myocarditis (KEGG):05416
4.94817686742777e-060.00052203265951363264Proteasome Degradation (Wikipathways):WP183
0.0003198274735665560.01557313775135612511Signaling in Immune system (Reactome):REACT_6900
3.12942733431072e-060.00044465996176429251{HLA-A,53} (Static Module):NA



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:0032393MHC class I receptor activity0.0216649005062993
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0236959849287649
GO:0048002antigen processing and presentation of peptide antigen0.0236959849287649
GO:0042612MHC class I protein complex0.039098375132462
GO:0042611MHC protein complex0.0468277797401782
GO:0019882antigen processing and presentation0.0468277797401782



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
leukocyte2.17e-31136
myeloid leukocyte7.60e-2772
nongranular leukocyte2.04e-26115
defensive cell2.88e-2548
phagocyte2.88e-2548
hematopoietic lineage restricted progenitor cell1.21e-24120
macrophage dendritic cell progenitor6.84e-2461
classical monocyte1.10e-2342
CD14-positive, CD16-negative classical monocyte1.10e-2342
monopoietic cell2.86e-2359
monocyte2.86e-2359
monoblast2.86e-2359
promonocyte2.86e-2359
granulocyte monocyte progenitor cell5.72e-2367
myeloid lineage restricted progenitor cell7.68e-2166
hematopoietic stem cell1.33e-18168
angioblastic mesenchymal cell1.33e-18168
hematopoietic oligopotent progenitor cell2.46e-18161
hematopoietic multipotent progenitor cell2.46e-18161
hematopoietic cell6.46e-18177
myeloid cell1.67e-13108
common myeloid progenitor1.67e-13108
stuff accumulating cell8.99e-1187
mesenchymal cell3.43e-08354
multi fate stem cell3.26e-07427
connective tissue cell3.26e-07361
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.33e-26108
hematopoietic system2.62e-2598
blood island2.62e-2598
immune system4.98e-2293
bone marrow5.87e-1976
bone element9.88e-1882
lateral plate mesoderm1.71e-15203
skeletal element1.74e-1390
skeletal system4.21e-11100
mesoderm7.16e-09315
mesoderm-derived structure7.16e-09315
presumptive mesoderm7.16e-09315
musculoskeletal system5.03e-07167
connective tissue6.73e-07371


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.11.90116
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.13.15662
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.11.29138
MA0259.10.575594
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
IRF4#3662214.60967512449610.006056122473217890.0268575530777241
NFKB1#479035.488063424193840.006049381815655430.0270713594757579
NFYA#4800212.28372046655370.008516011403724430.0324967560010806
NFYB#4801211.17319550235760.01025467135054530.0381596102465473
RFX5#5993312.04791082719510.0005717246050312580.00486517933878103



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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