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

Latest revision as of 10:47, 17 September 2013


Full id: C166_Macrophage_Monocytederived_Dendritic_adipose_lymph_CD14_lung



Phase1 CAGE Peaks

Hg19::chr10:80737664..80737698,-p@chr10:80737664..80737698
-
Hg19::chr10:82173423..82173439,+p5@FAM213A
Hg19::chr10:82173440..82173452,+p11@FAM213A
Hg19::chr11:118087684..118087694,-p@chr11:118087684..118087694
-
Hg19::chr11:118087713..118087733,-p@chr11:118087713..118087733
-
Hg19::chr11:118087749..118087766,-p@chr11:118087749..118087766
-
Hg19::chr11:122650064..122650075,+p15@UBASH3B
Hg19::chr11:122650109..122650120,+p14@UBASH3B
Hg19::chr11:122650146..122650175,+p10@UBASH3B
Hg19::chr11:128774561..128774596,-p1@C11orf45
Hg19::chr11:21934096..21934106,+p@chr11:21934096..21934106
+
Hg19::chr11:21934119..21934129,+p@chr11:21934119..21934129
+
Hg19::chr11:21934135..21934146,+p@chr11:21934135..21934146
+
Hg19::chr11:22174975..22174980,+p@chr11:22174975..22174980
+
Hg19::chr11:58959504..58959511,+p@chr11:58959504..58959511
+
Hg19::chr11:58959543..58959563,+p@chr11:58959543..58959563
+
Hg19::chr11:58959610..58959620,+p@chr11:58959610..58959620
+
Hg19::chr11:60718699..60718724,-p13@SLC15A3
Hg19::chr11:60719430..60719439,-p24@SLC15A3
Hg19::chr11:62344767..62344782,-p3@TUT1
Hg19::chr11:63964388..63964398,+p16@STIP1
Hg19::chr11:63964439..63964450,+p14@STIP1
Hg19::chr12:14721192..14721202,-p8@PLBD1
Hg19::chr12:16505660..16505685,-p@chr12:16505660..16505685
-
Hg19::chr12:26484990..26485000,-p@chr12:26484990..26485000
-
Hg19::chr12:4388020..4388039,+p9@CCND2
Hg19::chr12:4388045..4388063,+p18@CCND2
Hg19::chr12:49582225..49582269,-p7@TUBA1A
Hg19::chr12:53224364..53224373,-p2@KRT79
Hg19::chr12:56120803..56120814,-p38@CD63
Hg19::chr12:56120838..56120848,-p31@CD63
Hg19::chr13:113951188..113951191,+p21@LAMP1
Hg19::chr13:49086093..49086111,-p@chr13:49086093..49086111
-
Hg19::chr15:77308164..77308175,+p10@PSTPIP1
Hg19::chr15:77308178..77308193,+p11@PSTPIP1
Hg19::chr15:80469727..80469736,+p8@FAH
Hg19::chr15:80469741..80469772,+p6@FAH
Hg19::chr15:83779343..83779358,-p@chr15:83779343..83779358
-
Hg19::chr17:25958114..25958129,+p3@LGALS9
Hg19::chr17:4642833..4642875,-p3@CXCL16
Hg19::chr17:62315972..62315978,-p@chr17:62315972..62315978
-
Hg19::chr17:75276245..75276249,+p@chr17:75276245..75276249
+
Hg19::chr19:3785229..3785244,-p5@MATK
Hg19::chr19:3785250..3785292,-p3@MATK
Hg19::chr19:45418067..45418076,+p7@APOC1
Hg19::chr19:6680235..6680290,-p4@C3
Hg19::chr1:111050807..111050828,+p@chr1:111050807..111050828
+
Hg19::chr1:111050845..111050854,+p@chr1:111050845..111050854
+
Hg19::chr1:111052907..111052935,-p@chr1:111052907..111052935
-
Hg19::chr1:111058061..111058076,+p@chr1:111058061..111058076
+
Hg19::chr1:156510852..156510859,-p@chr1:156510852..156510859
-
Hg19::chr1:156510877..156510889,-p@chr1:156510877..156510889
-
Hg19::chr1:203155503..203155528,-p@chr1:203155503..203155528
-
Hg19::chr1:203198790..203198807,-p1@CHIT1
Hg19::chr1:27962025..27962032,-p15@FGR
Hg19::chr1:54707213..54707231,-p@chr1:54707213..54707231
-
Hg19::chr1:54707235..54707253,-p@chr1:54707235..54707253
-
Hg19::chr1:54707911..54707917,-p@chr1:54707911..54707917
-
Hg19::chr1:54707929..54707943,-p@chr1:54707929..54707943
-
Hg19::chr1:54707952..54707973,-p@chr1:54707952..54707973
-
Hg19::chr1:54707979..54707987,-p@chr1:54707979..54707987
-
Hg19::chr20:1875003..1875020,+p20@SIRPA
Hg19::chr20:33462829..33462852,+p5@ACSS2
Hg19::chr20:33462854..33462864,+p10@ACSS2
Hg19::chr20:33462888..33462894,+p12@ACSS2
Hg19::chr20:44645128..44645150,+p@chr20:44645128..44645150
+
Hg19::chr20:44645159..44645166,+p@chr20:44645159..44645166
+
Hg19::chr20:45179283..45179298,-p1@C20orf123
Hg19::chr2:217362648..217362677,+p3@RPL37A
Hg19::chr2:9562702..9562734,-p5@ITGB1BP1
Hg19::chr2:96782206..96782211,-p3@ADRA2B
Hg19::chr2:97012141..97012156,+p@chr2:97012141..97012156
+
Hg19::chr3:105717313..105717328,+p@chr3:105717313..105717328
+
Hg19::chr3:129334636..129334653,-p1@BC025331
Hg19::chr3:188665020..188665032,+p10@TPRG1
Hg19::chr3:196046974..196046977,-p@chr3:196046974..196046977
-
Hg19::chr3:196065248..196065267,-p1@TM4SF19
Hg19::chr4:48807155..48807187,+p13@OCIAD1
Hg19::chr4:682935..682946,-p2@MFSD7
Hg19::chr5:137330846..137330858,-p@chr5:137330846..137330858
-
Hg19::chr5:147789958..147789969,+p5@FBXO38
Hg19::chr6:160183931..160183971,+p@chr6:160183931..160183971
+
Hg19::chr6:164082461..164082467,-p@chr6:164082461..164082467
-
Hg19::chr6:164082471..164082476,-p@chr6:164082471..164082476
-
Hg19::chr6:164082477..164082487,-p@chr6:164082477..164082487
-
Hg19::chr6:33111201..33111222,-p1@HLA-DPA3
Hg19::chr6:4346987..4346998,-p@chr6:4346987..4346998
-
Hg19::chr6:4347006..4347027,-p@chr6:4347006..4347027
-
Hg19::chr6:46700055..46700067,-p@chr6:46700055..46700067
-
Hg19::chr7:128543401..128543428,-p2@KCP
Hg19::chr7:137308..137321,+p@chr7:137308..137321
+
Hg19::chr7:137336..137341,+p@chr7:137336..137341
+
Hg19::chr7:139762438..139762447,-p4@PARP12
Hg19::chr7:150477549..150477560,-p@chr7:150477549..150477560
-
Hg19::chr7:73507534..73507583,+p2@LIMK1
Hg19::chr8:102216925..102216938,-p7@ZNF706
Hg19::chr8:105670277..105670285,-p@chr8:105670277..105670285
-
Hg19::chr8:18680942..18680953,-p@chr8:18680942..18680953
-
Hg19::chr8:87111132..87111146,+p1@ATP6V0D2
Hg19::chr9:115945404..115945413,-p@chr9:115945404..115945413
-
Hg19::chr9:124030049..124030099,+p7@GSN
Hg19::chr9:86983624..86983647,-p2@SLC28A3
Hg19::chr9:86983657..86983666,-p4@SLC28A3
Hg19::chr9:86983667..86983668,-p11@SLC28A3
Hg19::chrX:149867720..149867743,+p@chrX:149867720..149867743
+


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

p.valueFDRnGenesnPathwayName
6.08120276742328e-050.03849401351778944156Phagosome (KEGG):04145



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:0005765lysosomal membrane0.00512780967323701
GO:0005774vacuolar membrane0.00512780967323701
GO:0044437vacuolar part0.00512780967323701
GO:0005764lysosome0.00512780967323701
GO:0000323lytic vacuole0.00512780967323701
GO:0005773vacuole0.00743018613799899
GO:0045807positive regulation of endocytosis0.0110236329171431
GO:0030100regulation of endocytosis0.0329666922785616
GO:0048518positive regulation of biological process0.0329666922785616
GO:0051050positive regulation of transport0.0329666922785616
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0329666922785616
GO:0005737cytoplasm0.0329666922785616
GO:0005768endosome0.0329666922785616
GO:0050265RNA uridylyltransferase activity0.0329666922785616
GO:0010324membrane invagination0.0329666922785616
GO:0006897endocytosis0.0329666922785616
GO:0005770late endosome0.037051496732088
GO:0001798positive regulation of type IIa hypersensitivity0.0419341731288713
GO:0002894positive regulation of type II hypersensitivity0.0419341731288713
GO:0001796regulation of type IIa hypersensitivity0.0419341731288713
GO:0002886regulation of myeloid leukocyte mediated immunity0.0419341731288713
GO:0002445type II hypersensitivity0.0419341731288713
GO:0001794type IIa hypersensitivity0.0419341731288713
GO:0002888positive regulation of myeloid leukocyte mediated immunity0.0419341731288713
GO:0002892regulation of type II hypersensitivity0.0419341731288713
GO:0048522positive regulation of cellular process0.0424802110626503
GO:0016044membrane organization and biogenesis0.0424802110626503
GO:0005534galactose binding0.0424802110626503
GO:0002712regulation of B cell mediated immunity0.0424802110626503
GO:0002863positive regulation of inflammatory response to antigenic stimulus0.0424802110626503
GO:0002885positive regulation of hypersensitivity0.0424802110626503
GO:0002866positive regulation of acute inflammatory response to antigenic stimulus0.0424802110626503
GO:0002675positive regulation of acute inflammatory response0.0424802110626503
GO:0002889regulation of immunoglobulin mediated immune response0.0424802110626503
GO:0002891positive regulation of immunoglobulin mediated immune response0.0424802110626503
GO:0002714positive regulation of B cell mediated immunity0.0424802110626503
GO:0045737positive regulation of cyclin-dependent protein kinase activity0.0424802110626503
GO:0051179localization0.0427484246496105
GO:0044440endosomal part0.0427484246496105
GO:0010008endosome membrane0.0427484246496105
GO:0004713protein-tyrosine kinase activity0.0427484246496105
GO:0048247lymphocyte chemotaxis0.0427484246496105
GO:0051014actin filament severing0.0427484246496105
GO:0002861regulation of inflammatory response to antigenic stimulus0.0427484246496105
GO:0002673regulation of acute inflammatory response0.0427484246496105
GO:0004938alpha2-adrenergic receptor activity0.0427484246496105
GO:0002864regulation of acute inflammatory response to antigenic stimulus0.0427484246496105
GO:0002883regulation of hypersensitivity0.0427484246496105
GO:0004334fumarylacetoacetase activity0.0427484246496105
GO:0051258protein polymerization0.0446980703271029
GO:0005415nucleoside:sodium symporter activity0.0484642556070935
GO:0006572tyrosine catabolic process0.0484642556070935
GO:0008061chitin binding0.0484642556070935
GO:0001882nucleoside binding0.0484642556070935
GO:0051049regulation of transport0.049824750361269
GO:0044464cell part0.049824750361269
GO:0045773positive regulation of axon extension0.049824750361269
GO:0002437inflammatory response to antigenic stimulus0.049824750361269
GO:0016823hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances0.049824750361269
GO:0002524hypersensitivity0.049824750361269
GO:0016822hydrolase activity, acting on acid carbon-carbon bonds0.049824750361269
GO:0015198oligopeptide transporter activity0.049824750361269
GO:0002438acute inflammatory response to antigenic stimulus0.049824750361269



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>

Uber Anatomy
Ontology termp-valuen
lower lobe of right lung3.91e-191
right lung lobe3.91e-191
lower lobe of lung3.91e-191
lobe of lung3.91e-191
right lung3.91e-191
bone marrow1.22e-1476
bone element1.50e-1382
skeletal element2.56e-1290
immune system6.57e-1293
hematopoietic system2.78e-1198
blood island2.78e-1198
skeletal system4.75e-11100
hemolymphoid system3.35e-10108


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)
MA0003.11.5016e-07
MA0004.10.0102141
MA0006.10.0227073
MA0007.10.410725
MA0009.10.621204
MA0014.15.77483e-05
MA0017.10.931513
MA0019.10.743836
MA0024.10.0515938
MA0025.10.152426
MA0027.11.42172
MA0028.17.43878e-05
MA0029.10.0576109
MA0030.10.199171
MA0031.10.14382
MA0038.10.0983453
MA0040.10.215556
MA0041.10.0442294
MA0042.10.077011
MA0043.10.0890602
MA0046.11.0083
MA0048.10.416569
MA0050.10.157318
MA0051.10.204699
MA0052.10.060786
MA0055.10.139465
MA0056.10
MA0057.10.0228124
MA0058.10.0269398
MA0059.10.322496
MA0060.10.00315494
MA0061.11.47103
MA0063.10
MA0066.10.376188
MA0067.10.265212
MA0068.10.17344
MA0069.10.282463
MA0070.10.0786216
MA0071.10.970523
MA0072.10.265509
MA0073.10.0750566
MA0074.10.363831
MA0076.10.00284478
MA0077.10.257351
MA0078.10.928097
MA0081.11.66629
MA0083.11.0622
MA0084.10.403089
MA0087.10.262908
MA0088.10.497905
MA0089.10
MA0090.11.06178
MA0091.13.60014
MA0092.10.36164
MA0093.10.000519286
MA0095.10
MA0098.10
MA0100.10.00724498
MA0101.10.103539
MA0103.10.332741
MA0105.10.268977
MA0106.10.134914
MA0107.10.592077
MA0108.20.141424
MA0109.10
MA0111.11.15289
MA0113.10.305295
MA0114.10.309241
MA0115.10.215224
MA0116.10.345831
MA0117.10.105084
MA0119.10.0983249
MA0122.10.752024
MA0124.10.189889
MA0125.10.142939
MA0130.10
MA0131.10.0847475
MA0132.10
MA0133.10
MA0135.10.101865
MA0136.10.885997
MA0139.10.0214164
MA0140.10.464206
MA0141.11.35395
MA0142.10.287194
MA0143.10.151498
MA0144.10.0371684
MA0145.10.242148
MA0146.10.00144203
MA0147.10.0154291
MA0148.10.554588
MA0149.10.0195608
MA0062.20.243443
MA0035.20.0678882
MA0039.21.22422e-05
MA0138.20.0752035
MA0002.20.89048
MA0137.20.0704286
MA0104.20.017072
MA0047.20.445002
MA0112.20.315121
MA0065.21.92813
MA0150.10.578198
MA0151.10
MA0152.10.162693
MA0153.10.418129
MA0154.10.835362
MA0155.10.0638412
MA0156.10.638465
MA0157.10.101395
MA0158.10
MA0159.10.173998
MA0160.10.609332
MA0161.10
MA0162.10.000450162
MA0163.10.00946896
MA0164.10.327908
MA0080.22.59785
MA0018.20.049435
MA0099.20.715803
MA0079.26.67433e-06
MA0102.20.432633
MA0258.10.695232
MA0259.10.0394238
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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