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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:27, 17 September 2013


Full id: C623_Dendritic_Neutrophils_Eosinophils_Whole_Macrophage_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr11:85779986..85780014,-p3@PICALM
Hg19::chr11:85780015..85780042,-p2@PICALM
Hg19::chr12:15114191..15114233,-p5@ARHGDIB
Hg19::chr12:8276205..8276219,+p2@CLEC4A
Hg19::chr12:8276224..8276237,+p3@CLEC4A
Hg19::chr14:93581500..93581509,-p12@ITPK1
Hg19::chr16:28192360..28192372,-p3@AB384470
Hg19::chr16:31271322..31271339,+p2@ITGAM
Hg19::chr16:8738211..8738249,+p@chr16:8738211..8738249
+
Hg19::chr16:8738462..8738501,+p@chr16:8738462..8738501
+
Hg19::chr16:90023641..90023698,+p@chr16:90023641..90023698
+
Hg19::chr3:149531627..149531651,+p7@RNF13
Hg19::chr5:142193841..142193874,+p@chr5:142193841..142193874
+
Hg19::chr8:38662960..38663003,+p9@TACC1


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:0035300inositol trisphosphate 5/6-kinase activity0.0113730683144134
GO:0043647inositol phosphate metabolic process0.0113730683144134
GO:0051765inositol tetrakisphosphate kinase activity0.0113730683144134
GO:0032957inositol trisphosphate metabolic process0.0113730683144134
GO:0047325inositol tetrakisphosphate 1-kinase activity0.0113730683144134
GO:0022610biological adhesion0.0142547691685994
GO:0007155cell adhesion0.0142547691685994
GO:0001948glycoprotein binding0.0213169715519573
GO:0048268clathrin cage assembly0.0227340873511213
GO:0006901vesicle coating0.0227340873511213
GO:0006900membrane budding0.02324871800575
GO:0030276clathrin binding0.0260425749057417
GO:0006020inositol metabolic process0.0266215290817958
GO:0051766inositol trisphosphate kinase activity0.0266215290817958
GO:0031410cytoplasmic vesicle0.0266215290817958
GO:0031982vesicle0.0266215290817958
GO:0016050vesicle organization and biogenesis0.0266215290817958
GO:0000287magnesium ion binding0.0266215290817958
GO:0005545phosphatidylinositol binding0.0269705183200261
GO:0005094Rho GDP-dissociation inhibitor activity0.0269705183200261
GO:0007162negative regulation of cell adhesion0.0351278293777307
GO:0005092GDP-dissociation inhibitor activity0.036104050016986
GO:0006898receptor-mediated endocytosis0.0487274734501486
GO:0044459plasma membrane part0.0487274734501486
GO:0005905coated pit0.0487274734501486



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 leukocyte3.78e-6672
macrophage dendritic cell progenitor2.71e-6261
monopoietic cell2.09e-6059
monocyte2.09e-6059
monoblast2.09e-6059
promonocyte2.09e-6059
defensive cell4.41e-5748
phagocyte4.41e-5748
granulocyte monocyte progenitor cell1.73e-5667
myeloid lineage restricted progenitor cell1.88e-5366
classical monocyte1.12e-4942
CD14-positive, CD16-negative classical monocyte1.12e-4942
leukocyte2.84e-42136
myeloid cell1.39e-41108
common myeloid progenitor1.39e-41108
nongranular leukocyte1.74e-34115
hematopoietic lineage restricted progenitor cell1.37e-31120
hematopoietic stem cell6.35e-31168
angioblastic mesenchymal cell6.35e-31168
hematopoietic cell5.75e-28177
hematopoietic oligopotent progenitor cell6.07e-28161
hematopoietic multipotent progenitor cell6.07e-28161
stuff accumulating cell3.03e-2487
intermediate monocyte6.56e-129
CD14-positive, CD16-positive monocyte6.56e-129
granulocyte2.49e-118
macrophage1.39e-086
immature conventional dendritic cell3.87e-085
common dendritic progenitor3.87e-085
blood cell1.26e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.43e-5998
blood island2.43e-5998
hemolymphoid system1.36e-54108
bone marrow3.25e-4776
immune system2.63e-4393
bone element3.53e-4282
skeletal element1.57e-3690
adult organism1.82e-34114
skeletal system4.93e-32100
lateral plate mesoderm4.74e-22203
musculoskeletal system4.21e-15167
blood1.13e-1115
haemolymphatic fluid1.13e-1115
organism substance1.13e-1115
mesoderm3.81e-11315
mesoderm-derived structure3.81e-11315
presumptive mesoderm3.81e-11315
neural tube2.22e-0856
neural rod2.22e-0856
future spinal cord2.22e-0856
neural keel2.22e-0856
tissue8.71e-08773
germ layer1.10e-07560
germ layer / neural crest1.10e-07560
embryonic tissue1.10e-07560
presumptive structure1.10e-07560
germ layer / neural crest derived structure1.10e-07560
epiblast (generic)1.10e-07560
embryonic structure2.15e-07564
regional part of nervous system5.45e-0753
regional part of brain5.45e-0753
telencephalon5.98e-0734
developing anatomical structure7.68e-07581


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)
MA0003.10.210327
MA0004.11.38635
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.11.10943
MA0017.10.181071
MA0019.12.74728
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.110534
MA0050.10.265714
MA0051.10.944936
MA0052.10.623986
MA0055.10.148782
MA0056.10
MA0057.10.0243088
MA0058.12.44274
MA0059.10.57771
MA0060.10.0773489
MA0061.11.27348
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.288906
MA0074.10.358953
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.11.72153
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.491738
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.11.46617
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.92504
MA0103.10.146091
MA0105.10.430023
MA0106.10.399649
MA0107.10.708233
MA0108.20.540797
MA0109.10
MA0111.11.23076
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.11.71931
MA0139.10.789887
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.11.06513
MA0144.10.652118
MA0145.10.547424
MA0146.10.0121843
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.473181
MA0035.20.326883
MA0039.20.0567934
MA0138.21.13988
MA0002.20.248488
MA0137.20.168782
MA0104.20.265556
MA0047.21.00935
MA0112.20.30305
MA0065.20.0634018
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.219649
MA0155.10.283527
MA0156.11.55848
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.10.00929209
MA0163.10.0498121
MA0164.10.425415
MA0080.22.10447
MA0018.20.400879
MA0099.20.333432
MA0079.20.211527
MA0102.21.22472
MA0258.10.624652
MA0259.10.374338
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
NFE2#4778211.02918009308990.01376231735648680.0484452682056733
SPI1#668874.102161754261360.0006255544805661120.005149545550236



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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