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Coexpression cluster:C3023: Difference between revisions

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{{Coexpression_clusters
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gonad development!0.0257906972704573!8031$GO:0050681!androgen receptor binding!0.0257906972704573!8031$GO:0046546!development of primary male sexual characteristics!0.0257906972704573!8031$GO:0035258!steroid hormone receptor binding!0.0257906972704573!8031$GO:0046661!male sex differentiation!0.0257906972704573!8031$GO:0030521!androgen receptor signaling pathway!0.0257906972704573!8031$GO:0030518!steroid hormone receptor signaling pathway!0.0257906972704573!8031$GO:0008406!gonad development!0.0257906972704573!8031$GO:0048608!reproductive structure development!0.0257906972704573!8031$GO:0030522!intracellular receptor-mediated signaling pathway!0.0257906972704573!8031$GO:0035257!nuclear hormone receptor binding!0.0257906972704573!8031$GO:0051427!hormone receptor binding!0.0257906972704573!8031$GO:0045137!development of primary sexual characteristics!0.0257906972704573!8031$GO:0007548!sex differentiation!0.0323204795991889!8031$GO:0003006!reproductive developmental 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|full_id=C3023_Whole_CD14_Reticulocytes_Neutrophils_blood_Eosinophils_immature
|id=C3023
}}

Latest revision as of 12:17, 17 September 2013


Full id: C3023_Whole_CD14_Reticulocytes_Neutrophils_blood_Eosinophils_immature



Phase1 CAGE Peaks

Hg19::chr10:51572408..51572454,+p3@NCOA4
Hg19::chr13:27745913..27745924,-p2@USP12
Hg19::chr13:27745936..27745961,-p1@USP12


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:0008584male gonad development0.0257906972704573
GO:0050681androgen receptor binding0.0257906972704573
GO:0046546development of primary male sexual characteristics0.0257906972704573
GO:0035258steroid hormone receptor binding0.0257906972704573
GO:0046661male sex differentiation0.0257906972704573
GO:0030521androgen receptor signaling pathway0.0257906972704573
GO:0030518steroid hormone receptor signaling pathway0.0257906972704573
GO:0008406gonad development0.0257906972704573
GO:0048608reproductive structure development0.0257906972704573
GO:0030522intracellular receptor-mediated signaling pathway0.0257906972704573
GO:0035257nuclear hormone receptor binding0.0257906972704573
GO:0051427hormone receptor binding0.0257906972704573
GO:0045137development of primary sexual characteristics0.0257906972704573
GO:0007548sex differentiation0.0323204795991889
GO:0003006reproductive developmental process0.0323974185904191
GO:0004221ubiquitin thiolesterase activity0.0431014388996514
GO:0004843ubiquitin-specific protease activity0.0431014388996514
GO:0019783small conjugating protein-specific protease activity0.0431014388996514



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 leukocyte1.12e-3072
granulocyte monocyte progenitor cell2.23e-2867
myeloid lineage restricted progenitor cell6.80e-2866
myeloid cell3.82e-26108
common myeloid progenitor3.82e-26108
macrophage dendritic cell progenitor1.39e-2561
defensive cell8.76e-2548
phagocyte8.76e-2548
monopoietic cell2.51e-2459
monocyte2.51e-2459
monoblast2.51e-2459
promonocyte2.51e-2459
leukocyte5.15e-23136
classical monocyte6.26e-2342
CD14-positive, CD16-negative classical monocyte6.26e-2342
hematopoietic stem cell2.03e-20168
angioblastic mesenchymal cell2.03e-20168
hematopoietic oligopotent progenitor cell3.46e-19161
hematopoietic multipotent progenitor cell3.46e-19161
hematopoietic lineage restricted progenitor cell1.13e-18120
hematopoietic cell2.18e-18177
nongranular leukocyte1.44e-15115
stuff accumulating cell2.97e-1087
mesenchymal cell1.30e-08354
connective tissue cell4.04e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.24e-3098
blood island1.24e-3098
hemolymphoid system8.71e-28108
bone marrow1.86e-2376
bone element3.51e-2282
immune system1.72e-1993
skeletal element3.99e-1890
skeletal system2.46e-16100
lateral plate mesoderm1.12e-14203
blood1.64e-1015
haemolymphatic fluid1.64e-1015
organism substance1.64e-1015
mesoderm5.81e-10315
mesoderm-derived structure5.81e-10315
presumptive mesoderm5.81e-10315
connective tissue8.92e-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)
MA0003.110.3157
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.15032
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
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
MA0073.12.26659
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.846801
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.11.37817
MA0146.14.51393
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.90173
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
CTCF#1066435.360256373075030.0064925092527670.0278183045681942
E2F1#186934.907389214879320.008460985347239390.0323399520085029
E2F6#187635.017155731697390.00791769806886330.032023718868175
EBF1#187938.9064668465690.00141523283560980.00912379642705261
EGR1#195834.988179094810140.008056488137383440.0318933956705401
ELF1#199734.258097958807540.01295179875054610.0459842571970453
MYC#460935.22228187160940.007020843755740150.0293077221713796
PAX5#507936.669565531177830.003370290999677260.0172206370702198
RAD21#5885310.35503389545630.0009004912073565420.00661599727084839
SP1#666735.69838137814090.005403962701712170.0245331215215874
YY1#752834.911170749853860.008441455341808260.0327787460753686
ZBTB7A#5134137.35190930787590.002516255860282270.0139576824831113



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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