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{{Coexpression_clusters
{
|full_id=C979_Mast_CD14_Eosinophils_immature_Neutrophils_CD4_Basophils
|

Latest revision as of 11:35, 17 September 2013


Full id: C979_Mast_CD14_Eosinophils_immature_Neutrophils_CD4_Basophils



Phase1 CAGE Peaks

Hg19::chr10:35484090..35484104,+p6@CREM
Hg19::chr14:91976671..91976682,-p6@SMEK1
Hg19::chr15:52313600..52313611,+p12@MAPK6
Hg19::chr16:80404220..80404224,+p@chr16:80404220..80404224
+
Hg19::chr1:178569076..178569079,+p@chr1:178569076..178569079
+
Hg19::chr21:36260463..36260480,-p9@RUNX1
Hg19::chr3:182971089..182971100,+p12@B3GNT5
Hg19::chr3:182971130..182971148,+p3@B3GNT5


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:0008457beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity0.0057400211939244
GO:0030854positive regulation of granulocyte differentiation0.0057400211939244
GO:0008917lipopolysaccharide N-acetylglucosaminyltransferase activity0.0057400211939244
GO:0030852regulation of granulocyte differentiation0.0057400211939244
GO:0008140cAMP response element binding protein binding0.0137744288177509
GO:0030851granulocyte differentiation0.0153040198506013
GO:0002763positive regulation of myeloid leukocyte differentiation0.0157923462251457
GO:0016563transcription activator activity0.0157923462251457
GO:0045766positive regulation of angiogenesis0.0286764594625967
GO:0045639positive regulation of myeloid cell differentiation0.0286764594625967
GO:0009247glycolipid biosynthetic process0.0286764594625967
GO:0002761regulation of myeloid leukocyte differentiation0.0286764594625967
GO:0007275multicellular organismal development0.0334812275315464
GO:0006664glycolipid metabolic process0.0458310383064836
GO:0002573myeloid leukocyte differentiation0.0458310383064836
GO:0045637regulation of myeloid cell differentiation0.0458310383064836
GO:0004707MAP kinase activity0.0458310383064836
GO:0045765regulation of angiogenesis0.0482261591889499
GO:0008378galactosyltransferase activity0.0482261591889499



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
classical monocyte8.57e-3742
CD14-positive, CD16-negative classical monocyte8.57e-3742
myeloid leukocyte8.43e-3472
defensive cell1.48e-3348
phagocyte1.48e-3348
granulocyte monocyte progenitor cell5.58e-3367
myeloid lineage restricted progenitor cell2.22e-3066
macrophage dendritic cell progenitor1.08e-2961
monopoietic cell6.92e-2859
monocyte6.92e-2859
monoblast6.92e-2859
promonocyte6.92e-2859
myeloid cell1.80e-19108
common myeloid progenitor1.80e-19108
stuff accumulating cell7.48e-1987
leukocyte2.03e-16136
hematopoietic lineage restricted progenitor cell6.76e-13120
nongranular leukocyte3.54e-11115
hematopoietic stem cell1.44e-10168
angioblastic mesenchymal cell1.44e-10168
hematopoietic cell1.71e-09177
hematopoietic oligopotent progenitor cell5.86e-09161
hematopoietic multipotent progenitor cell5.86e-09161
Uber Anatomy
Ontology termp-valuen
immune system1.18e-2993
bone marrow2.36e-2976
bone element5.84e-2782
skeletal element7.57e-2690
hemolymphoid system7.81e-26108
hematopoietic system2.39e-2498
blood island2.39e-2498
skeletal system3.65e-21100
musculoskeletal system8.19e-13167
lateral plate mesoderm3.30e-10203
mesoderm5.05e-07315
mesoderm-derived structure5.05e-07315
presumptive mesoderm5.05e-07315


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)
MA0003.10.140538
MA0004.10.455723
MA0006.11.47431
MA0007.10.437331
MA0009.10.918715
MA0014.10.727045
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.11.2107
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.11.28413
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.82745
MA0145.10.220937
MA0146.10.0399277
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.44475
MA0138.20.653421
MA0002.20.531206
MA0137.21.55178
MA0104.20.189646
MA0047.20.586412
MA0112.20.208783
MA0065.20.0631316
MA0150.11.77699
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.764865
MA0156.10.865715
MA0157.11.66465
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.11.29519
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.21.29876
MA0079.20.200187
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
EGR1#195853.117611934256340.01051390990388360.038925954002329
FOSL2#235536.348825226710630.009211946658641070.0348279212670799
STAT1#677237.76497031144970.005248673889186180.024314315915401



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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