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{{Coexpression_clusters
{
|full_id=C250_Mast_Neutrophils_CD14_Eosinophils_CD8_Peripheral_CD4
 

Latest revision as of 11:06, 17 September 2013


Full id: C250_Mast_Neutrophils_CD14_Eosinophils_CD8_Peripheral_CD4



Phase1 CAGE Peaks

Hg19::chr10:3826687..3826699,-p@chr10:3826687..3826699
-
Hg19::chr16:27325702..27325750,-p@chr16:27325702..27325750
-
Hg19::chr16:27325969..27325994,+p@chr16:27325969..27325994
+
Hg19::chr17:38506028..38506044,+p@chr17:38506028..38506044
+
Hg19::chr19:13264446..13264492,+p3@IER2
Hg19::chr19:13953130..13953158,-p@chr19:13953130..13953158
-
Hg19::chr19:39897051..39897070,+p3@ZFP36
Hg19::chr19:39898470..39898488,+p@chr19:39898470..39898488
+
Hg19::chr19:39898498..39898514,+p@chr19:39898498..39898514
+
Hg19::chr19:39898523..39898532,+p@chr19:39898523..39898532
+
Hg19::chr19:39898544..39898598,+p@chr19:39898544..39898598
+
Hg19::chr19:39898599..39898666,+p@chr19:39898599..39898666
+
Hg19::chr19:39898678..39898692,-p@chr19:39898678..39898692
-
Hg19::chr19:39898695..39898725,-p@chr19:39898695..39898725
-
Hg19::chr19:39898701..39898712,+p@chr19:39898701..39898712
+
Hg19::chr19:39898715..39898729,+p@chr19:39898715..39898729
+
Hg19::chr19:39898746..39898756,+p@chr19:39898746..39898756
+
Hg19::chr19:39898760..39898777,+p@chr19:39898760..39898777
+
Hg19::chr19:39898772..39898888,-p1@CU679444
Hg19::chr19:39898781..39898796,+p@chr19:39898781..39898796
+
Hg19::chr19:39898814..39898855,+p@chr19:39898814..39898855
+
Hg19::chr19:39898896..39898901,+p@chr19:39898896..39898901
+
Hg19::chr19:39898940..39898958,+p@chr19:39898940..39898958
+
Hg19::chr19:39898968..39898980,+p@chr19:39898968..39898980
+
Hg19::chr19:39898988..39899013,+p@chr19:39898988..39899013
+
Hg19::chr19:39899024..39899036,+p@chr19:39899024..39899036
+
Hg19::chr19:39899079..39899097,+p@chr19:39899079..39899097
+
Hg19::chr19:39899258..39899276,+p@chr19:39899258..39899276
+
Hg19::chr19:39899297..39899308,+p@chr19:39899297..39899308
+
Hg19::chr19:39899540..39899551,+p2@AJ227917
Hg19::chr19:39899566..39899574,-p8@CU679444
Hg19::chr19:39899597..39899634,+p1@AJ227917
Hg19::chr19:39899887..39899894,+p4@AJ227917
Hg19::chr1:204380074..204380108,-p8@PPP1R15B
Hg19::chr3:128445232..128445249,+p@chr3:128445232..128445249
+
Hg19::chr3:39186740..39186774,-p@chr3:39186740..39186774
-
Hg19::chr3:39188204..39188217,-p3@CU691620
Hg19::chr5:172195219..172195236,-p3@AJ227912
Hg19::chr5:172195778..172195809,+p@chr5:172195778..172195809
+
Hg19::chr5:172195833..172195881,-p2@AJ227912
Hg19::chr5:172195883..172195911,-p4@AJ227912
Hg19::chr5:172195926..172195937,-p13@AJ227912
Hg19::chr5:172195979..172196000,-p6@AJ227912
Hg19::chr5:172196072..172196092,-p5@AJ227912
Hg19::chr5:172196095..172196120,-p1@AJ227912
Hg19::chr5:172196608..172196676,-p@chr5:172196608..172196676
-
Hg19::chr5:172196683..172196802,-p@chr5:172196683..172196802
-
Hg19::chr5:172197180..172197212,-p2@AK127679
Hg19::chr5:172197219..172197279,-p1@AK127679
Hg19::chr5:172197282..172197310,-p3@AK127679
Hg19::chr6:35310813..35310823,+p@chr6:35310813..35310823
+
Hg19::chr8:38645035..38645076,+p11@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:0017091AU-rich element binding0.00447427293064877
GO:0000289poly(A) tail shortening0.00447427293064877
GO:0050779RNA destabilization0.00447427293064877
GO:0000288mRNA catabolic process, deadenylation-dependent decay0.0134180779336029
GO:0043487regulation of RNA stability0.0134180779336029
GO:0043488regulation of mRNA stability0.0134180779336029
GO:0004726non-membrane spanning protein tyrosine phosphatase activity0.0134180779336029
GO:0031348negative regulation of defense response0.0134180779336029
GO:0050728negative regulation of inflammatory response0.0134180779336029
GO:0031124mRNA 3'-end processing0.0167644521049474
GO:0033549MAP kinase phosphatase activity0.0167644521049474
GO:0017017MAP kinase tyrosine/serine/threonine phosphatase activity0.0167644521049474
GO:0045638negative regulation of myeloid cell differentiation0.0167644521049474
GO:0031123RNA 3'-end processing0.0167644521049474
GO:0051252regulation of RNA metabolic process0.0167644521049474
GO:0003727single-stranded RNA binding0.0167644521049474
GO:0031347regulation of defense response0.0186230565034739
GO:0050727regulation of inflammatory response0.0186230565034739
GO:0006402mRNA catabolic process0.0201572588362358
GO:0007049cell cycle0.0201572588362358
GO:0045637regulation of myeloid cell differentiation0.0203953832529684
GO:0003729mRNA binding0.0203953832529684
GO:0048583regulation of response to stimulus0.0203953832529684
GO:0006401RNA catabolic process0.0256759940779331
GO:0006950response to stress0.032222988276366
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.032222988276366
GO:0045596negative regulation of cell differentiation0.032222988276366
GO:0030099myeloid cell differentiation0.035520473619963
GO:0051093negative regulation of developmental process0.035520473619963



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
classical monocyte2.00e-3342
CD14-positive, CD16-negative classical monocyte2.00e-3342
defensive cell4.76e-2848
phagocyte4.76e-2848
myeloid leukocyte7.43e-2772
leukocyte1.71e-24136
granulocyte monocyte progenitor cell2.21e-2167
macrophage dendritic cell progenitor5.84e-2161
monopoietic cell1.31e-1959
monocyte1.31e-1959
monoblast1.31e-1959
promonocyte1.31e-1959
myeloid lineage restricted progenitor cell1.94e-1966
hematopoietic lineage restricted progenitor cell8.83e-17120
nongranular leukocyte1.35e-16115
stuff accumulating cell2.49e-1587
hematopoietic stem cell8.27e-14168
angioblastic mesenchymal cell8.27e-14168
myeloid cell3.72e-13108
common myeloid progenitor3.72e-13108
hematopoietic cell1.52e-12177
hematopoietic oligopotent progenitor cell2.21e-12161
hematopoietic multipotent progenitor cell2.21e-12161
granulocyte1.86e-088
intermediate monocyte3.71e-089
CD14-positive, CD16-positive monocyte3.71e-089
connective tissue cell7.17e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.95e-2598
blood island6.95e-2598
hemolymphoid system1.73e-22108
bone marrow4.07e-1976
immune system1.37e-1793
skeletal element1.55e-1790
bone element3.47e-1782
skeletal system8.22e-16100
adult organism1.31e-12114
lateral plate mesoderm3.05e-08203


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)
MA0003.14.6469
MA0004.10.0271967
MA0006.10.0817273
MA0007.10.100157
MA0009.10.247013
MA0014.10.129448
MA0017.10.431162
MA0019.10.0728369
MA0024.10.179268
MA0025.10.344113
MA0027.11.7227
MA0028.10.0325527
MA0029.10.191103
MA0030.10.184045
MA0031.10.146399
MA0038.10.0561953
MA0040.10.194748
MA0041.10.128556
MA0042.10.103967
MA0043.10.24723
MA0046.10.239588
MA0048.13.22224
MA0050.10.10461
MA0051.10.20146
MA0052.10.197173
MA0055.18.51304
MA0056.10
MA0057.10.877503
MA0058.10.0108543
MA0059.10.0106968
MA0060.11.37418
MA0061.10.873386
MA0063.10
MA0066.10.45332
MA0067.10.492893
MA0068.10.0304489
MA0069.10.236979
MA0070.10.229464
MA0071.10.16802
MA0072.10.22647
MA0073.10.333946
MA0074.10.773385
MA0076.10.0129251
MA0077.10.221371
MA0078.10.0938727
MA0081.10.0530098
MA0083.10.70251
MA0084.10.656589
MA0087.10.224848
MA0088.11.13366
MA0089.10
MA0090.10.0700587
MA0091.11.62619
MA0092.10.0887874
MA0093.10.00497579
MA0095.10
MA0098.10
MA0100.10.0610601
MA0101.11.09255
MA0103.10.490042
MA0105.10.925139
MA0106.11.89138
MA0107.10.681777
MA0108.20.444542
MA0109.10
MA0111.12.20169
MA0113.10.0778665
MA0114.11.17307
MA0115.10.42937
MA0116.12.72167
MA0117.10.273271
MA0119.10.996978
MA0122.10.793402
MA0124.10.395861
MA0125.10.330489
MA0130.10
MA0131.10.334679
MA0132.10
MA0133.10
MA0135.10.268144
MA0136.10.0586412
MA0139.10.00694278
MA0140.10.043016
MA0141.10.0520676
MA0142.10.129252
MA0143.10.0779387
MA0144.10.584557
MA0145.11.54878
MA0146.11.54227
MA0147.10.0973808
MA0148.10.033106
MA0149.10.0402234
MA0062.20.308856
MA0035.20.0428087
MA0039.20.304888
MA0138.20.647598
MA0002.21.26126
MA0137.20.00650365
MA0104.20.0436235
MA0047.20.0666578
MA0112.27.83177
MA0065.21.85069
MA0150.10.0666548
MA0151.10
MA0152.11.06559
MA0153.10.317813
MA0154.10.559572
MA0155.15.36079
MA0156.10.0358831
MA0157.10.115269
MA0158.10
MA0159.10.192614
MA0160.10.146686
MA0161.10
MA0162.10.000365872
MA0163.11.4339
MA0164.10.592353
MA0080.20.0279968
MA0018.20.25124
MA0099.20.0450826
MA0079.20.00104316
MA0102.20.690195
MA0258.12.29705
MA0259.10.0132572
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
CCNT2#905151.827750454893070.01240073781131270.0448930866330094
EBF1#1879233.939398797520911.8712595866431e-091.61915890612609e-07
HEY1#23462211.631583305869610.009367003429565320.0353514426039957
PAX5#5079202.565217511991473.10097941821131e-050.000628250610006927
POLR2A#5430502.064858823613539.85681600402904e-151.70719072412071e-12
USF2#7392266.49609869253487.30629970006958e-161.38486866492843e-13



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

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