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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:08, 17 September 2013


Full id: C260_acute_chronic_Natural_NK_Basophils_biphenotypic_blood



Phase1 CAGE Peaks

Hg19::chr14:101165430..101165451,-p@chr14:101165430..101165451
-
Hg19::chr14:47722173..47722192,-p@chr14:47722173..47722192
-
Hg19::chr15:54267149..54267170,-p1@ENST00000558920
Hg19::chr15:54267188..54267200,-p2@ENST00000558920
Hg19::chr15:95398778..95398792,+p3@ENST00000556065
Hg19::chr17:55531631..55531640,+p@chr17:55531631..55531640
+
Hg19::chr17:78994695..78994737,-p@chr17:78994695..78994737
-
Hg19::chr18:71468395..71468399,+p@chr18:71468395..71468399
+
Hg19::chr1:1118144..1118151,-p@chr1:1118144..1118151
-
Hg19::chr1:198979759..198979783,-p@chr1:198979759..198979783
-
Hg19::chr1:198999872..198999874,-p@chr1:198999872..198999874
-
Hg19::chr1:208078141..208078145,+p@chr1:208078141..208078145
+
Hg19::chr1:208084565..208084567,+p@chr1:208084565..208084567
+
Hg19::chr1:208084930..208084934,-p22@CD34
Hg19::chr20:25913764..25913768,+p@chr20:25913764..25913768
+
Hg19::chr20:60881514..60881520,+p@chr20:60881514..60881520
+
Hg19::chr2:103038624..103038629,+p@chr2:103038624..103038629
+
Hg19::chr2:127851262..127851291,-p@chr2:127851262..127851291
-
Hg19::chr2:129468319..129468326,-p@chr2:129468319..129468326
-
Hg19::chr2:166651029..166651044,-p11@GALNT3
Hg19::chr2:58967795..58967809,-p@chr2:58967795..58967809
-
Hg19::chr2:71766260..71766282,+p@chr2:71766260..71766282
+
Hg19::chr3:196365912..196365930,+p@chr3:196365912..196365930
+
Hg19::chr4:164871108..164871113,-p@chr4:164871108..164871113
-
Hg19::chr5:118217409..118217420,-p@chr5:118217409..118217420
-
Hg19::chr5:118219344..118219349,-p@chr5:118219344..118219349
-
Hg19::chr5:30850137..30850150,-p@chr5:30850137..30850150
-
Hg19::chr6:12957376..12957395,+p31@PHACTR1
Hg19::chr6:12957417..12957446,+p20@PHACTR1
Hg19::chr6:12957811..12957820,+p37@PHACTR1
Hg19::chr6:30029672..30029686,+p@chr6:30029672..30029686
+
Hg19::chr6:49792450..49792465,-p1@uc003ozv.1
Hg19::chr6:49792495..49792498,-p1@ENST00000430821
Hg19::chr6:5866096..5866110,+p@chr6:5866096..5866110
+
Hg19::chr7:117426647..117426651,-p@chr7:117426647..117426651
-
Hg19::chr7:1274988..1274991,+p@chr7:1274988..1274991
+
Hg19::chr7:1275077..1275088,+p@chr7:1275077..1275088
+
Hg19::chr7:38316320..38316349,-p3@TARP
Hg19::chr7:38358560..38358567,-p2@TRGV9
Hg19::chr7:38358578..38358595,-p1@TRGV9
Hg19::chr7:38370591..38370600,+p@chr7:38370591..38370600
+
Hg19::chr7:38370618..38370628,+p@chr7:38370618..38370628
+
Hg19::chr7:38370646..38370667,+p@chr7:38370646..38370667
+
Hg19::chr7:38370708..38370720,+p@chr7:38370708..38370720
+
Hg19::chr7:73752953..73752964,+p@chr7:73752953..73752964
+
Hg19::chr8:108340337..108340344,+p@chr8:108340337..108340344
+
Hg19::chr8:142555259..142555264,-p@chr8:142555259..142555264
-
Hg19::chr8:142555285..142555291,-p@chr8:142555285..142555291
-
Hg19::chr8:142555297..142555302,-p@chr8:142555297..142555302
-
Hg19::chr8:60173723..60173754,+p@chr8:60173723..60173754
+
Hg19::chr8:82598191..82598195,-p3@IMPA1


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:0008934inositol-1(or 4)-monophosphatase activity0.026484607892999
GO:0031403lithium ion binding0.026484607892999
GO:0006661phosphatidylinositol biosynthetic process0.026484607892999
GO:0030246carbohydrate binding0.0316981286456445
GO:0042605peptide antigen binding0.0316981286456445
GO:0004653polypeptide N-acetylgalactosaminyltransferase activity0.0316981286456445
GO:0044459plasma membrane part0.0316981286456445
GO:0042287MHC protein binding0.0316981286456445
GO:0046488phosphatidylinositol metabolic process0.0316981286456445
GO:0008376acetylgalactosaminyltransferase activity0.0316981286456445
GO:0050900leukocyte migration0.0316981286456445
GO:0004864protein phosphatase inhibitor activity0.0316981286456445
GO:0019212phosphatase inhibitor activity0.0316981286456445
GO:0046489phosphoinositide biosynthetic process0.0316981286456445
GO:0005975carbohydrate metabolic process0.0316981286456445
GO:0046474glycerophospholipid biosynthetic process0.0379820699667983
GO:0009897external side of plasma membrane0.0388471879066574
GO:0004437inositol or phosphatidylinositol phosphatase activity0.041808238422943
GO:0044425membrane part0.0470009140373129
GO:0019888protein phosphatase regulator activity0.0470009140373129
GO:0030384phosphoinositide metabolic process0.0470009140373129
GO:0005886plasma membrane0.0470009140373129
GO:0019208phosphatase regulator activity0.0470009140373129



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><br><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia7.41e-0831


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)
MA0003.10.000156995
MA0004.10.840732
MA0006.10.0290142
MA0007.10.256778
MA0009.10.252434
MA0014.11.02032e-06
MA0017.10.0446111
MA0019.10.0757474
MA0024.10.183969
MA0025.10.350278
MA0027.11.73105
MA0028.10.38452
MA0029.10.570205
MA0030.10.55303
MA0031.10.459469
MA0038.10.213125
MA0040.11.09698
MA0041.10.575636
MA0042.10.793334
MA0043.10.252653
MA0046.10.24494
MA0048.10.0103142
MA0050.10.49669
MA0051.10.458113
MA0052.10.584895
MA0055.10.167661
MA0056.10
MA0057.10.00288364
MA0058.11.12025
MA0059.10.790284
MA0060.10.0480936
MA0061.10.349228
MA0063.10
MA0066.10.467033
MA0067.10.49981
MA0068.10.322801
MA0069.10.242306
MA0070.10.661924
MA0071.10.174636
MA0072.10.231695
MA0073.18.15667e-06
MA0074.10.0569489
MA0076.10.572984
MA0077.10.226543
MA0078.11.61911
MA0081.10.790955
MA0083.13.72248
MA0084.10.664025
MA0087.10.230056
MA0088.10.405217
MA0089.10
MA0090.10.07398
MA0091.10.534615
MA0092.10.441881
MA0093.11.4519
MA0095.10
MA0098.10
MA0100.11.28434
MA0101.10.567753
MA0103.10.511293
MA0105.10.103423
MA0106.10.257854
MA0107.10.711338
MA0108.20.45517
MA0109.10
MA0111.10.403858
MA0113.10.276654
MA0114.10.475868
MA0115.10.436009
MA0116.10.332304
MA0117.10.27892
MA0119.11.38212
MA0122.10.297683
MA0124.11.03875
MA0125.10.336564
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.10.27375
MA0136.11.75344
MA0139.10.190948
MA0140.11.06745
MA0141.10.0552982
MA0142.10.133251
MA0143.10.582117
MA0144.10.26716
MA0145.10.0814484
MA0146.10.132027
MA0147.10.342831
MA0148.12.3103
MA0149.10.0422402
MA0062.20.871386
MA0035.20.688657
MA0039.20.00430244
MA0138.20.0978028
MA0002.20.798153
MA0137.20.107881
MA0104.20.307315
MA0047.21.34586
MA0112.20.0678886
MA0065.20.292957
MA0150.11.2514
MA0151.10
MA0152.10.178362
MA0153.10.323801
MA0154.10.0975962
MA0155.10.210981
MA0156.11.24236
MA0157.10.76104
MA0158.10
MA0159.10.527617
MA0160.10.152819
MA0161.10
MA0162.15.33183e-05
MA0163.10.000511528
MA0164.11.02028
MA0080.22.70722
MA0018.20.0747401
MA0099.20.709941
MA0079.21.4428e-08
MA0102.20.697711
MA0258.10.384507
MA0259.10.11442
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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