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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:35, 17 September 2013


Full id: C983_CD19_CD14_immature_Eosinophils_Natural_CD8_Neutrophils



Phase1 CAGE Peaks

Hg19::chr10:75173389..75173414,+p@chr10:75173389..75173414
+
Hg19::chr12:70133272..70133287,-p@chr12:70133272..70133287
-
Hg19::chr1:207495270..207495305,+p10@CD55
Hg19::chr5:100240379..100240385,+p@chr5:100240379..100240385
+
Hg19::chr6:14118396..14118415,+p@chr6:14118396..14118415
+
Hg19::chr6:14118443..14118457,+p@chr6:14118443..14118457
+
Hg19::chr6:14119773..14119779,+p@chr6:14119773..14119779
+
Hg19::chr6:14131244..14131255,+p@chr6:14131244..14131255
+


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

No GOStat results

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
leukocyte2.45e-95136
hematopoietic lineage restricted progenitor cell2.05e-75120
hematopoietic stem cell1.08e-73168
angioblastic mesenchymal cell1.08e-73168
nongranular leukocyte4.05e-71115
hematopoietic cell5.82e-71177
hematopoietic oligopotent progenitor cell1.26e-70161
hematopoietic multipotent progenitor cell1.26e-70161
classical monocyte2.70e-6642
CD14-positive, CD16-negative classical monocyte2.70e-6642
myeloid leukocyte1.29e-6472
granulocyte monocyte progenitor cell6.17e-5867
defensive cell1.30e-5648
phagocyte1.30e-5648
myeloid lineage restricted progenitor cell7.41e-5366
macrophage dendritic cell progenitor3.36e-5261
myeloid cell5.75e-49108
common myeloid progenitor5.75e-49108
monopoietic cell3.63e-4859
monocyte3.63e-4859
monoblast3.63e-4859
promonocyte3.63e-4859
stuff accumulating cell2.24e-2687
mesenchymal cell4.57e-26354
connective tissue cell3.44e-25361
motile cell4.16e-22386
intermediate monocyte4.07e-219
CD14-positive, CD16-positive monocyte4.07e-219
lymphoid lineage restricted progenitor cell1.40e-1852
multi fate stem cell2.44e-18427
lymphocyte4.17e-1853
common lymphoid progenitor4.17e-1853
stem cell6.03e-18441
somatic stem cell8.06e-18433
nucleate cell3.28e-1755
Langerhans cell6.80e-125
conventional dendritic cell1.26e-118
lymphocyte of B lineage6.52e-1124
pro-B cell6.52e-1124
granulocyte1.15e-108
dendritic cell2.60e-0910
somatic cell1.65e-08588
natural killer cell3.35e-083
pro-NK cell3.35e-083
histamine secreting cell3.48e-085
biogenic amine secreting cell3.48e-085
granulocytopoietic cell3.48e-085
mast cell3.48e-085
mast cell progenitor3.48e-085
basophil mast progenitor cell3.48e-085
single nucleate cell3.97e-083
mononuclear cell3.97e-083
basophil1.02e-073
blood cell1.58e-0711
non-classical monocyte2.33e-073
CD14-low, CD16-positive monocyte2.33e-073
Uber Anatomy
Ontology termp-valuen
bone marrow1.25e-4976
bone element4.25e-4582
hematopoietic system7.31e-4498
blood island7.31e-4498
hemolymphoid system2.52e-40108
immune system3.56e-4093
skeletal element5.42e-4090
skeletal system9.29e-35100
connective tissue5.37e-24371
musculoskeletal system5.59e-16167
lateral plate mesoderm1.91e-14203


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)
MA0003.10.576745
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.473479
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.11.92084
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
MA0055.10.835832
MA0056.10
MA0057.10.305162
MA0058.10.950944
MA0059.10.948176
MA0060.10.190336
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.466265
MA0074.10.552456
MA0076.10.985027
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.291333
MA0105.11.47197
MA0106.10.59853
MA0107.11.23931
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.11.25157
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
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.0613434
MA0146.10.0399277
MA0147.10.681318
MA0148.11.20731
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.164269
MA0138.20.653421
MA0002.21.01797
MA0137.20.321796
MA0104.21.05746
MA0047.21.43258
MA0112.20.208783
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.141536
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.0909775
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
E2F6#187663.762866798773040.001207680027997810.0081880611817751
EBF1#187944.45323342328450.007651884996748980.0315174008982279
NFKB1#479064.116047568145380.0007299856589784310.00581710455043861
POLR2A#543082.147453176558070.002210725788971910.0127301092062875
TRIM28#1015536.971446891973450.007100847201045050.0296073690845554



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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