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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.204373122013994,

Latest revision as of 12:37, 17 September 2013


Full id: C4022_CD14_Eosinophils_Neutrophils_Basophils_migratory_epidermoid_Mast



Phase1 CAGE Peaks

Hg19::chr20:31407751..31407795,+p1@MAPRE1
Hg19::chr8:101964198..101964221,-p2@YWHAZ
Hg19::chr8:101964231..101964255,-p1@YWHAZ


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:0031115negative regulation of microtubule polymerization0.00506284401442095
GO:0030981cortical microtubule cytoskeleton0.00506284401442095
GO:0051010microtubule plus-end binding0.00506284401442095
GO:0031113regulation of microtubule polymerization0.0101246447580706
GO:0046785microtubule polymerization0.0101246447580706
GO:0048523negative regulation of cellular process0.0140589016358978
GO:0048519negative regulation of biological process0.0140589016358978
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0140589016358978
GO:0030863cortical cytoskeleton0.0140589016358978
GO:0031110regulation of microtubule polymerization or depolymerization0.0146766288835239
GO:0031109microtubule polymerization or depolymerization0.0147219867739274
GO:0044448cell cortex part0.0187912866763938
GO:0008017microtubule binding0.0187912866763938
GO:0051129negative regulation of cellular component organization and biogenesis0.0187912866763938
GO:0005938cell cortex0.0209860622386991
GO:0015631tubulin binding0.0209860622386991
GO:0008022protein C-terminus binding0.0209860622386991
GO:0005819spindle0.0209860622386991
GO:0048770pigment granule0.0209860622386991
GO:0042470melanosome0.0209860622386991
GO:0051258protein polymerization0.0224198953551073
GO:0051128regulation of cellular component organization and biogenesis0.0224198953551073
GO:0000226microtubule cytoskeleton organization and biogenesis0.0224198953551073
GO:0019904protein domain specific binding0.0267419858021847
GO:0006916anti-apoptosis0.0343427151346421
GO:0043066negative regulation of apoptosis0.0411992843938898
GO:0043069negative regulation of programmed cell death0.0411992843938898
GO:0007067mitosis0.0411992843938898
GO:0000087M phase of mitotic cell cycle0.0411992843938898
GO:0051301cell division0.0411992843938898
GO:0005874microtubule0.0466903559920029
GO:0000279M phase0.0466903559920029
GO:0044444cytoplasmic part0.0466903559920029
GO:0007017microtubule-based process0.0466903559920029
GO:0000278mitotic cell cycle0.0469325831757985
GO:0016023cytoplasmic membrane-bound vesicle0.0479180146242358
GO:0031988membrane-bound vesicle0.0479180146242358
GO:0022403cell cycle phase0.0488980343754735



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
leukocyte4.17e-28136
classical monocyte1.80e-2542
CD14-positive, CD16-negative classical monocyte1.80e-2542
myeloid leukocyte5.71e-2572
defensive cell1.23e-2248
phagocyte1.23e-2248
granulocyte monocyte progenitor cell2.79e-2067
macrophage dendritic cell progenitor8.98e-2061
nongranular leukocyte9.00e-20115
hematopoietic lineage restricted progenitor cell1.48e-19120
stuff accumulating cell3.66e-1987
monopoietic cell4.49e-1959
monocyte4.49e-1959
monoblast4.49e-1959
promonocyte4.49e-1959
myeloid lineage restricted progenitor cell2.74e-1866
native cell1.47e-15722
hematopoietic stem cell2.00e-14168
angioblastic mesenchymal cell2.00e-14168
hematopoietic oligopotent progenitor cell1.15e-13161
hematopoietic multipotent progenitor cell1.15e-13161
animal cell5.52e-13679
eukaryotic cell5.52e-13679
hematopoietic cell2.11e-12177
somatic stem cell1.48e-11433
stem cell3.80e-11441
multi fate stem cell4.06e-11427
myeloid cell5.74e-11108
common myeloid progenitor5.74e-11108
somatic cell3.53e-10588
mesenchymal cell2.08e-09354
motile cell4.40e-09386
connective tissue cell4.24e-08361
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.29e-1798
blood island1.29e-1798
hemolymphoid system3.30e-15108
bone marrow8.76e-1576
bone element3.65e-1482
skeletal element2.28e-1390
skeletal system4.35e-13100
immune system2.34e-1293
musculoskeletal system6.16e-09167
connective tissue1.12e-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)
MA0003.10.401049
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.11.70014
MA0060.13.15662
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
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
MA0101.11.55947
MA0103.10.628063
MA0105.10.31555
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
MA0131.12.4174
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
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
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
BRCA1#672213.45615376214920.007119807716084560.0296284654763579
CCNT2#90536.336201576962630.003930750035764890.0190286271894525
E2F1#186934.907389214879320.008460985347239390.0325820157324706
E2F6#187635.017155731697390.00791769806886330.0322736893534468
EGR1#195834.988179094810140.008056488137383440.0321100429163559
FOS#235338.99795530889440.001372499272417130.00898473433069904
FOSL2#2355316.93020060456170.0002060162053171620.00243257506694393
HMGN3#932438.178547723350590.001827766942164210.0108831329345889
IRF1#365937.63716375356390.002244692747297240.0128245878465523
JUND#372736.994663941871030.002921845042734990.0156972517704835
MAX#414936.452555509007120.003721913834265510.0186809380496374
NANOG#79923219.49651898734180.003427255648501020.0174510824764174
NFYA#4800318.42558069983050.0001598135507814160.00199889430300124
NFYB#4801316.75979325353650.0002123649923296180.00246189226705661
PAX5#507936.669565531177830.003370290999677260.0173095560223897
REST#597839.650028716128020.001112636247114590.00768688344330228
SREBF1#6720231.33723296032550.00133816265136180.00887623811658148
TCF7L2#6934310.77017656313730.0008003181298398380.00614455819762868
USF1#739136.361499277207960.00388404057290560.0190560113399581



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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