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

Latest revision as of 11:22, 17 September 2013


Full id: C407_Neutrophils_CD14_Eosinophils_Peripheral_CD19_CD4_Natural



Phase1 CAGE Peaks

Hg19::chr10:14641848..14641853,-p@chr10:14641848..14641853
-
Hg19::chr10:65028665..65028674,-p17@JMJD1C
Hg19::chr10:70848483..70848488,+p@chr10:70848483..70848488
+
Hg19::chr11:78029412..78029415,-p@chr11:78029412..78029415
-
Hg19::chr11:78127822..78127826,-p@chr11:78127822..78127826
-
Hg19::chr12:10279509..10279514,-p4@CLEC7A
Hg19::chr12:65057642..65057645,+p@chr12:65057642..65057645
+
Hg19::chr12:90064720..90064735,-p@chr12:90064720..90064735
-
Hg19::chr14:100842126..100842137,+p@chr14:100842126..100842137
+
Hg19::chr14:70149688..70149690,+p@chr14:70149688..70149690
+
Hg19::chr15:51047821..51047824,-p@chr15:51047821..51047824
-
Hg19::chr17:49187745..49187750,-p@chr17:49187745..49187750
-
Hg19::chr19:10389255..10389259,+p@chr19:10389255..10389259
+
Hg19::chr20:48315901..48315905,-p@chr20:48315901..48315905
-
Hg19::chr20:5590491..5590495,-p@chr20:5590491..5590495
-
Hg19::chr20:5590556..5590620,-p@chr20:5590556..5590620
-
Hg19::chr2:114691822..114691837,+p3@ACTR3
Hg19::chr2:114692625..114692632,+p@chr2:114692625..114692632
+
Hg19::chr2:131867907..131867911,+p@chr2:131867907..131867911
+
Hg19::chr2:145263063..145263073,-p@chr2:145263063..145263073
-
Hg19::chr2:201984578..201984581,+p@chr2:201984578..201984581
+
Hg19::chr2:37876585..37876589,-p@chr2:37876585..37876589
-
Hg19::chr2:64367919..64367920,-p@chr2:64367919..64367920
-
Hg19::chr4:103423374..103423399,+p@chr4:103423374..103423399
+
Hg19::chr5:90679281..90679304,+p@chr5:90679281..90679304
+


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:0009756carbohydrate mediated signaling0.0133550151197745
GO:0006910phagocytosis, recognition0.0133550151197745
GO:0042832defense response to protozoan0.0133550151197745
GO:0001562response to protozoan0.0133550151197745
GO:0005885Arp2/3 protein complex0.0149567362972983
GO:0008329pattern recognition receptor activity0.0213636212234457
GO:0009743response to carbohydrate stimulus0.0274626613699662
GO:0042287MHC protein binding0.0296603415103792
GO:0046966thyroid hormone receptor binding0.0296603415103792
GO:0005102receptor binding0.033105752264889
GO:0008037cell recognition0.0336600330303587
GO:0030027lamellipodium0.0336600330303587
GO:0006909phagocytosis0.0336600330303587
GO:0035257nuclear hormone receptor binding0.040537128657825
GO:0051427hormone receptor binding0.040537128657825
GO:0010033response to organic substance0.0413311162716758
GO:0031252leading edge0.0426417620285896
GO:0051213dioxygenase activity0.0426417620285896
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0426417620285896
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0426417620285896
GO:0042110T cell activation0.0497223462987851



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
leukocyte4.76e-57136
nongranular leukocyte2.27e-46115
hematopoietic lineage restricted progenitor cell2.94e-46120
hematopoietic stem cell2.00e-45168
angioblastic mesenchymal cell2.00e-45168
hematopoietic oligopotent progenitor cell3.63e-44161
hematopoietic multipotent progenitor cell3.63e-44161
myeloid leukocyte9.19e-4472
hematopoietic cell1.16e-43177
granulocyte monocyte progenitor cell5.19e-3767
classical monocyte5.14e-3642
CD14-positive, CD16-negative classical monocyte5.14e-3642
macrophage dendritic cell progenitor3.07e-3561
myeloid lineage restricted progenitor cell1.09e-3466
defensive cell2.60e-3448
phagocyte2.60e-3448
monopoietic cell7.26e-3459
monocyte7.26e-3459
monoblast7.26e-3459
promonocyte7.26e-3459
myeloid cell4.52e-31108
common myeloid progenitor4.52e-31108
stuff accumulating cell7.15e-1387
lymphocyte1.27e-1153
common lymphoid progenitor1.27e-1153
lymphoid lineage restricted progenitor cell2.67e-1152
nucleate cell1.01e-1055
intermediate monocyte1.27e-089
CD14-positive, CD16-positive monocyte1.27e-089
granulocyte1.87e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.06e-4398
blood island4.06e-4398
hemolymphoid system4.53e-38108
bone marrow8.01e-3276
immune system2.40e-2993
bone element2.28e-2882
skeletal element1.73e-2390
skeletal system6.21e-20100
lateral plate mesoderm6.17e-12203
blood9.45e-1015
haemolymphatic fluid9.45e-1015
organism substance9.45e-1015
adult organism9.44e-09114


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)
MA0003.11.71169e-05
MA0004.10.130779
MA0006.10.0525289
MA0007.10.120068
MA0009.10.480543
MA0014.10.00927576
MA0017.10.242343
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.11.0498
MA0030.10.397801
MA0031.10.344829
MA0038.10.195728
MA0040.11.06051
MA0041.12.00108
MA0042.11.2704
MA0043.10.480818
MA0046.10.47108
MA0048.10.055058
MA0050.10.390696
MA0051.10.562815
MA0052.11.0676
MA0055.10.0658753
MA0056.10
MA0057.10.0501
MA0058.10.0802423
MA0059.10.0796335
MA0060.10.017391
MA0061.10.317574
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.11.2121
MA0069.10.467738
MA0070.10.458064
MA0071.10.170069
MA0072.10.454189
MA0073.10.0379112
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.263604
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.0164834
MA0089.10
MA0090.10.0951695
MA0091.10.132307
MA0092.10.357807
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.44587
MA0103.10.411939
MA0105.10.0399898
MA0106.10.224407
MA0107.10.539977
MA0108.20.342362
MA0109.10
MA0111.10.102187
MA0113.10.236174
MA0114.10.118114
MA0115.10.697973
MA0116.10.030864
MA0117.10.513502
MA0119.10.0722294
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.200538
MA0139.10.0510937
MA0140.10.971518
MA0141.10.270862
MA0142.10.319458
MA0143.10.665621
MA0144.10.104952
MA0145.10.349442
MA0146.10.0020729
MA0147.10.031895
MA0148.10.876759
MA0149.10.162171
MA0062.20.0113502
MA0035.20.969659
MA0039.20.000132971
MA0138.20.264522
MA0002.20.182759
MA0137.20.481909
MA0104.20.0172311
MA0047.21.16012
MA0112.20.0502653
MA0065.20.126603
MA0150.10.307678
MA0151.10
MA0152.10.988857
MA0153.10.567879
MA0154.10.0935732
MA0155.10.0441847
MA0156.10.0625308
MA0157.10.298026
MA0158.10
MA0159.10.307966
MA0160.10.154993
MA0161.10
MA0162.10.000165262
MA0163.10.00408849
MA0164.10.245213
MA0080.20.0537406
MA0018.20.225392
MA0099.20.514256
MA0079.28.45205e-08
MA0102.20.983247
MA0258.10.239173
MA0259.10.138164
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
WRNIP1#56897313.17839572192510.001492358232376610.0095432525980395



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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