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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:31, 17 September 2013


Full id: C803_Macrophage_CD14_Monocytederived_Eosinophils_Basophils_CD14CD16_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:58980342..58980431,-p1@MPEG1
Hg19::chr13:51289225..51289244,-p@chr13:51289225..51289244
-
Hg19::chr14:103587774..103587784,+p@chr14:103587774..103587784
+
Hg19::chr15:51914996..51915035,-p2@DMXL2
Hg19::chr20:1472164..1472175,-p3@SIRPB2
Hg19::chr5:140012540..140012567,-p8@CD14
Hg19::chr5:140012752..140012768,-p1@CD14
Hg19::chr5:140012773..140012794,-p2@CD14
Hg19::chr7:139529007..139529038,+p3@TBXAS1
Hg19::chrX:37639302..37639326,+p1@CYBB


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:0009611response to wounding0.00259656563361436
GO:0009605response to external stimulus0.00432029297768241
GO:0004796thromboxane-A synthase activity0.0135397656327913
GO:0006950response to stress0.0151692776269214
GO:0006954inflammatory response0.016921717954316
GO:0016019peptidoglycan receptor activity0.016921717954316
GO:0042834peptidoglycan binding0.0203000847796423
GO:0046457prostanoid biosynthetic process0.0203000847796423
GO:0002237response to molecule of bacterial origin0.0203000847796423
GO:0001516prostaglandin biosynthetic process0.0203000847796423
GO:0008329pattern recognition receptor activity0.0221429395266416
GO:0005506iron ion binding0.0244276827821287
GO:0006693prostaglandin metabolic process0.0245847341859006
GO:0006692prostanoid metabolic process0.0245847341859006
GO:0044459plasma membrane part0.0245847341859006
GO:0006952defense response0.0245847341859006
GO:0017137Rab GTPase binding0.0322090574849813
GO:0006118electron transport0.0334093525836169
GO:0046456icosanoid biosynthetic process0.0352103301235468
GO:0006909phagocytosis0.0415392895817162
GO:0045121lipid raft0.0421923624208418
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.0421923624208418
GO:0006091generation of precursor metabolites and energy0.0421923624208418
GO:0006690icosanoid metabolic process0.0421923624208418



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 leukocyte6.84e-5372
monopoietic cell4.80e-4759
monocyte4.80e-4759
monoblast4.80e-4759
promonocyte4.80e-4759
defensive cell5.09e-4648
phagocyte5.09e-4648
macrophage dendritic cell progenitor1.17e-4461
granulocyte monocyte progenitor cell9.47e-4467
myeloid lineage restricted progenitor cell2.08e-4366
classical monocyte6.60e-4042
CD14-positive, CD16-negative classical monocyte6.60e-4042
leukocyte1.43e-37136
myeloid cell1.18e-33108
common myeloid progenitor1.18e-33108
nongranular leukocyte2.05e-33115
hematopoietic stem cell7.73e-31168
angioblastic mesenchymal cell7.73e-31168
hematopoietic lineage restricted progenitor cell9.08e-30120
hematopoietic oligopotent progenitor cell7.21e-28161
hematopoietic multipotent progenitor cell7.21e-28161
hematopoietic cell2.22e-27177
stuff accumulating cell1.35e-1887
intermediate monocyte3.01e-099
CD14-positive, CD16-positive monocyte3.01e-099
granulocyte2.76e-088
macrophage2.20e-076
Uber Anatomy
Ontology termp-valuen
adult organism7.25e-48114
hematopoietic system7.23e-4598
blood island7.23e-4598
hemolymphoid system2.66e-40108
bone marrow1.45e-3676
immune system3.23e-3393
bone element5.59e-3282
skeletal element7.03e-2790
skeletal system2.21e-23100
neural tube1.99e-1756
neural rod1.99e-1756
future spinal cord1.99e-1756
neural keel1.99e-1756
regional part of nervous system9.20e-1653
regional part of brain9.20e-1653
lateral plate mesoderm2.49e-15203
regional part of forebrain3.05e-1441
forebrain3.05e-1441
anterior neural tube3.05e-1441
future forebrain3.05e-1441
telencephalon2.04e-1234
brain grey matter3.34e-1234
gray matter3.34e-1234
central nervous system1.27e-1181
brain2.20e-1168
future brain2.20e-1168
regional part of telencephalon2.89e-1132
cerebral hemisphere3.15e-1132
tissue1.56e-10773
neural plate2.13e-1082
presumptive neural plate2.13e-1082
regional part of cerebral cortex2.26e-0922
neurectoderm2.89e-0986
organ4.81e-09503
nervous system4.93e-0989
neocortex2.31e-0820
musculoskeletal system4.38e-08167
germ layer5.00e-08560
germ layer / neural crest5.00e-08560
embryonic tissue5.00e-08560
presumptive structure5.00e-08560
germ layer / neural crest derived structure5.00e-08560
epiblast (generic)5.00e-08560
blood1.12e-0715
haemolymphatic fluid1.12e-0715
organism substance1.12e-0715
embryonic structure1.23e-07564
cerebral cortex1.37e-0725
pallium1.37e-0725
pre-chordal neural plate2.27e-0761
basal ganglion8.66e-079
nuclear complex of neuraxis8.66e-079
aggregate regional part of brain8.66e-079
collection of basal ganglia8.66e-079
cerebral subcortex8.66e-079


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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0216849
MA0017.11.36636
MA0019.10.520264
MA0024.10.725404
MA0025.13.62307
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.965046
MA0051.10.473017
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00294698
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.11.44489
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.189717
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.998594
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.11.51733
MA0145.10.14293
MA0146.10.0551603
MA0147.10.184931
MA0148.11.83679
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0317541
MA0138.20.569505
MA0002.20.129981
MA0137.20.710884
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.10.296882
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.162989
MA0164.11.34364
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.00952548
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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

No analysis results for this cluster

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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