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

Latest revision as of 11:05, 17 September 2013


Full id: C248_iPS_Aortic_Hep2_amygdala_acute_medial_Myoblast



Phase1 CAGE Peaks

Hg19::chr10:118316172..118316174,+p@chr10:118316172..118316174
+
Hg19::chr10:51371401..51371434,+p1@TIMM23B
Hg19::chr10:91738412..91738433,+p2@SNRPD2P1
Hg19::chr11:125937329..125937360,+p1@NAP1L1P1
Hg19::chr11:32113490..32113494,+p@chr11:32113490..32113494
+
Hg19::chr11:56457700..56457749,+p1@ENST00000530434
Hg19::chr11:74660278..74660334,+p1@SPCS2
Hg19::chr11:93268577..93268595,+p2@ENST00000533701
Hg19::chr11:93268598..93268609,+p3@ENST00000533701
Hg19::chr11:96930964..96930970,+p@chr11:96930964..96930970
+
Hg19::chr12:63396232..63396236,+p1@ENST00000546650
Hg19::chr12:6547635..6547653,+p1@ENST00000447193
Hg19::chr12:8786931..8786949,+p1@ENST00000540341
Hg19::chr16:28722774..28722807,+p1@EIF3CL
p1@EIF3C
Hg19::chr16:28722809..28722820,+p2@EIF3C
Hg19::chr16:81129886..81129900,-p2@GCSH
Hg19::chr17:64766837..64766855,+p@chr17:64766837..64766855
+
Hg19::chr18:60085536..60085538,+p@chr18:60085536..60085538
+
Hg19::chr19:47778489..47778503,+p4@PRR24
Hg19::chr1:147400526..147400541,+p1@GPR89A
p1@GPR89B
Hg19::chr1:160287068..160287094,+p1@SUMO1P3
Hg19::chr20:6194218..6194234,+p1@ENST00000434910
Hg19::chr2:202689240..202689246,+p1@ENST00000411559
Hg19::chr2:203043989..203044014,+p1@ENST00000429685
Hg19::chr2:215562319..215562343,+p1@ENSAP3
Hg19::chr2:219064995..219065012,+p2@HMGB1P9
Hg19::chr2:219065015..219065047,+p1@HMGB1P9
Hg19::chr2:26045115..26045120,+p1@ENST00000407942
Hg19::chr3:22423205..22423225,+p1@HMGB1P5
Hg19::chr3:96068204..96068231,+p1@HNRNPKP4
Hg19::chr4:11370223..11370243,+p1@MIR572
Hg19::chr4:190394055..190394060,+p1@HSP90AA4P
Hg19::chr4:68311705..68311712,+p1@ENST00000508720
Hg19::chr5:172952686..172952687,+p@chr5:172952686..172952687
+
Hg19::chr5:177302520..177302548,+p1@ENST00000506672
Hg19::chr5:31923423..31923442,+p3@ENST00000506046
Hg19::chr5:76878173..76878177,+p1@ENST00000493874
Hg19::chr6:147727578..147727589,+p1@YAP1P1
Hg19::chr6:29404662..29404683,+p@chr6:29404662..29404683
+
Hg19::chr6:34187145..34187149,+p1@CYCSP55
Hg19::chr7:10490855..10490865,+p1@ENST00000419827
Hg19::chr7:135335552..135335555,+p@chr7:135335552..135335555
+
Hg19::chr7:3740599..3740621,+p@chr7:3740599..3740621
+
Hg19::chr7:53574034..53574038,+p@chr7:53574034..53574038
+
Hg19::chr7:55799735..55799767,+p1@SUMO2P3
Hg19::chr7:5938386..5938430,+p1@CCZ1B
p1@CCZ1
Hg19::chr7:63895150..63895155,+p@chr7:63895150..63895155
+
Hg19::chr8:102381049..102381068,+p2@NACAP1
Hg19::chr8:146220249..146220272,+p1@TMED10P1
Hg19::chr8:71016502..71016506,-p1@ENST00000406023
p1@ENST00000521867
Hg19::chrX:33059434..33059464,+p2@TBCAP1
Hg19::chrX:33059467..33059499,+p1@TBCAP1
Hg19::chrX:68003226..68003229,+p1@ENST00000396021


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:0005852eukaryotic translation initiation factor 3 complex0.00023297493378405
GO:0006413translational initiation0.00704921342770137
GO:0003743translation initiation factor activity0.00704921342770137
GO:0022618protein-RNA complex assembly0.00709118496049346
GO:0008135translation factor activity, nucleic acid binding0.0110468791359476
GO:0043234protein complex0.0110468791359476
GO:0005787signal peptidase complex0.0110468791359476
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0110468791359476
GO:0032991macromolecular complex0.0263807899356535
GO:0009003signal peptidase activity0.0263807899356535
GO:0005744mitochondrial inner membrane presequence translocase complex0.0270512476685397
GO:0006465signal peptide processing0.0270512476685397
GO:0044444cytoplasmic part0.0333867519422573
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0333867519422573
GO:0022884macromolecule transmembrane transporter activity0.0333867519422573
GO:0008320protein transmembrane transporter activity0.0333867519422573
GO:0006518peptide metabolic process0.0333867519422573
GO:0065003macromolecular complex assembly0.0446612539727981
GO:0022607cellular component assembly0.0487153428619245



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 monocyte3.93e-2942
CD14-positive, CD16-negative classical monocyte3.93e-2942
defensive cell4.14e-2948
phagocyte4.14e-2948
myeloid lineage restricted progenitor cell2.14e-2466
granulocyte monocyte progenitor cell1.77e-2367
stuff accumulating cell7.76e-2387
macrophage dendritic cell progenitor5.05e-2261
myeloid leukocyte1.77e-2172
monopoietic cell1.70e-2059
monocyte1.70e-2059
monoblast1.70e-2059
promonocyte1.70e-2059
myeloid cell2.01e-20108
common myeloid progenitor2.01e-20108
hematopoietic lineage restricted progenitor cell2.43e-19120
leukocyte4.76e-19136
hematopoietic stem cell9.46e-18168
angioblastic mesenchymal cell9.46e-18168
hematopoietic oligopotent progenitor cell1.87e-17161
hematopoietic multipotent progenitor cell1.87e-17161
hematopoietic cell9.67e-16177
nongranular leukocyte6.50e-14115
stem cell3.55e-07441
multi fate stem cell7.49e-07427
Uber Anatomy
Ontology termp-valuen
bone marrow4.61e-2176
skeletal element1.28e-1890
bone element2.03e-1882
immune system3.96e-1793
skeletal system3.26e-15100
hematopoietic system8.95e-1498
blood island8.95e-1498
hemolymphoid system1.11e-12108
larynx1.83e-129
musculoskeletal system5.38e-09167


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)
MA0003.10.000291462
MA0004.10.025727
MA0006.10.311824
MA0007.10.0219097
MA0009.10.6783
MA0014.10.000512531
MA0017.10.039209
MA0019.11.35246
MA0024.10.174713
MA0025.10.89723
MA0027.11.7145
MA0028.11.84093
MA0029.10.547244
MA0030.11.01654
MA0031.10.862549
MA0038.10.439255
MA0040.11.05891
MA0041.15.25074
MA0042.14.19154
MA0043.10.241959
MA0046.10.234388
MA0048.10.547324
MA0050.10.0998136
MA0051.10.755485
MA0052.10.192408
MA0055.10.79366
MA0056.10
MA0057.10.0351877
MA0058.10.0100997
MA0059.10.280702
MA0060.10.0892507
MA0061.10.0247827
MA0063.10
MA0066.10.76873
MA0067.10.486134
MA0068.10.0274407
MA0069.10.231803
MA0070.10.224361
MA0071.10.161667
MA0072.10.221396
MA0073.14.43373e-05
MA0074.10.0521726
MA0076.10.808255
MA0077.10.618767
MA0078.10.303473
MA0081.10.482313
MA0083.10.246867
MA0084.11.56445
MA0087.11.1754
MA0088.10.121511
MA0089.10
MA0090.10.345107
MA0091.10.0262924
MA0092.10.410987
MA0093.10.00456335
MA0095.10
MA0098.10
MA0100.10.0585556
MA0101.10.327469
MA0103.10.0695571
MA0105.10.0109562
MA0106.10.0685575
MA0107.10.0836166
MA0108.20.14061
MA0109.10
MA0111.10.0742471
MA0113.10.260048
MA0114.10.0783923
MA0115.10.422889
MA0116.10.173991
MA0117.10.738418
MA0119.10.250266
MA0122.10.780586
MA0124.11.01081
MA0125.10.324569
MA0130.10
MA0131.10.668373
MA0132.10
MA0133.10
MA0135.13.76353
MA0136.10.205756
MA0139.10.0464908
MA0140.10.0410132
MA0141.10.277329
MA0142.10.125391
MA0143.10.260247
MA0144.10.134234
MA0145.10.0651497
MA0146.10.00415659
MA0147.10.0910812
MA0148.10.128204
MA0149.10.0383072
MA0062.21.27839
MA0035.20.363255
MA0039.21.70554e-05
MA0138.20.304949
MA0002.20.240441
MA0137.20.0326918
MA0104.20.0882662
MA0047.20.494964
MA0112.20.00678403
MA0065.20.0403766
MA0150.10.0630618
MA0151.10
MA0152.10.670208
MA0153.10.311979
MA0154.10.022693
MA0155.10.00199805
MA0156.10.0335364
MA0157.10.727679
MA0158.10
MA0159.10.01072
MA0160.10.596085
MA0161.10
MA0162.10.00169809
MA0163.13.7631e-05
MA0164.10.0800163
MA0080.20.0260344
MA0018.20.243347
MA0099.20.0430176
MA0079.21.92865e-16
MA0102.20.682839
MA0258.10.119218
MA0259.10.0414898
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

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