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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:37, 17 September 2013


Full id: C1092_Hepatic_CD8_CD4_Endothelial_Renal_lymph_spleen



Phase1 CAGE Peaks

Hg19::chr7:150147807..150147847,+p1@GIMAP8
Hg19::chr7:150147877..150147898,+p3@GIMAP8
Hg19::chr7:150147899..150147910,+p7@GIMAP8
Hg19::chr7:150147930..150147943,+p4@GIMAP8
Hg19::chr7:150329353..150329364,-p7@GIMAP6
Hg19::chr7:150329389..150329412,-p3@GIMAP6
Hg19::chr7:150329421..150329482,-p1@GIMAP6
Hg19::chr7:150329530..150329552,-p2@GIMAP6


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:0005525GTP binding0.00118477953347309
GO:0032561guanyl ribonucleotide binding0.00118477953347309
GO:0019001guanyl nucleotide binding0.00118477953347309
GO:0032553ribonucleotide binding0.0133979824776932
GO:0032555purine ribonucleotide binding0.0133979824776932
GO:0017076purine nucleotide binding0.0133979824776932
GO:0000166nucleotide binding0.0157508168628174



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
endothelial cell2.19e-2536
endothelial cell of vascular tree9.13e-2224
meso-epithelial cell2.50e-1745
blood vessel endothelial cell4.07e-1718
embryonic blood vessel endothelial progenitor cell4.07e-1718
defensive cell6.33e-1548
phagocyte6.33e-1548
nongranular leukocyte1.33e-13115
classical monocyte1.65e-1342
CD14-positive, CD16-negative classical monocyte1.65e-1342
monopoietic cell1.09e-1259
monocyte1.09e-1259
monoblast1.09e-1259
promonocyte1.09e-1259
mature alpha-beta T cell5.34e-1218
alpha-beta T cell5.34e-1218
immature T cell5.34e-1218
mature T cell5.34e-1218
immature alpha-beta T cell5.34e-1218
myeloid leukocyte5.93e-1272
macrophage dendritic cell progenitor7.83e-1261
myeloid lineage restricted progenitor cell1.17e-1166
hematopoietic lineage restricted progenitor cell1.19e-11120
leukocyte2.00e-11136
granulocyte monocyte progenitor cell2.81e-1167
lining cell1.80e-1058
barrier cell1.80e-1058
endothelial cell of artery2.02e-099
CD8-positive, alpha-beta T cell5.00e-0911
T cell2.74e-0825
pro-T cell2.74e-0825
hematopoietic stem cell8.25e-08168
angioblastic mesenchymal cell8.25e-08168
vein endothelial cell2.37e-076
hematopoietic oligopotent progenitor cell2.43e-07161
hematopoietic multipotent progenitor cell2.43e-07161
aortic endothelial cell5.36e-076
Uber Anatomy
Ontology termp-valuen
adult organism8.24e-47114
hemolymphoid system1.21e-19108
blood vessel endothelium4.07e-1718
endothelium4.07e-1718
cardiovascular system endothelium4.07e-1718
lateral plate mesoderm5.89e-17203
hematopoietic system8.67e-1698
blood island8.67e-1698
immune system1.63e-1493
simple squamous epithelium1.51e-1222
squamous epithelium3.84e-1025
endothelial tube2.02e-099
arterial system endothelium2.02e-099
endothelium of artery2.02e-099
bone marrow7.86e-0976
circulatory system2.14e-08112
neural tube4.52e-0856
neural rod4.52e-0856
future spinal cord4.52e-0856
neural keel4.52e-0856
cardiovascular system2.68e-07109
bone element2.79e-0782
regional part of nervous system3.42e-0753
regional part of brain3.42e-0753
anatomical conduit7.63e-07240
blood8.56e-0715
haemolymphatic fluid8.56e-0715
organism substance8.56e-0715


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)
MA0003.10.248189
MA0004.10.455723
MA0006.10.812175
MA0007.13.95452
MA0009.10.918715
MA0014.10.275152
MA0017.10.896777
MA0019.11.46622
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
MA0048.11.08711
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.93074
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.000871324
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
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
MA0105.10.279181
MA0106.10.59853
MA0107.11.23931
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
MA0122.12.25035
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.11.38624
MA0139.10.155155
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.239099
MA0147.10.681318
MA0148.12.09557
MA0149.13.22166
MA0062.21.50503
MA0035.20.515566
MA0039.20.00133745
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.20.458158
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.11.16939
MA0156.11.55957
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.11.23953
MA0161.10
MA0162.10.0752715
MA0163.10.0104024
MA0164.10.627336
MA0080.23.13741
MA0018.21.46097
MA0099.21.29876
MA0079.20.00346431
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
FOS#235344.49897765444720.007374489916227120.0304818281695826
POLR2A#543082.147453176558070.002210725788971910.0127266007427206
SPI1#668844.102161754261360.01027800662400760.0381920135844564



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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