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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: C431_acute_leukemia_Mast_leiomyoblastoma_chronic_immature_CD34



Phase1 CAGE Peaks

Hg19::chr11:58611957..58611975,-p2@GLYATL2
Hg19::chr12:116985635..116985640,-p@chr12:116985635..116985640
-
Hg19::chr12:116985694..116985708,-p@chr12:116985694..116985708
-
Hg19::chr18:45479920..45479950,-p@chr18:45479920..45479950
-
Hg19::chr1:230410128..230410174,+p@chr1:230410128..230410174
+
Hg19::chr1:230410177..230410188,+p@chr1:230410177..230410188
+
Hg19::chr1:246345465..246345467,-p@chr1:246345465..246345467
-
Hg19::chr1:246347752..246347761,-p@chr1:246347752..246347761
-
Hg19::chr1:246347797..246347809,-p@chr1:246347797..246347809
-
Hg19::chr1:246347830..246347835,-p@chr1:246347830..246347835
-
Hg19::chr1:246347998..246348004,-p@chr1:246347998..246348004
-
Hg19::chr1:246350179..246350186,-p@chr1:246350179..246350186
-
Hg19::chr1:246350204..246350229,-p@chr1:246350204..246350229
-
Hg19::chr1:246350240..246350281,-p@chr1:246350240..246350281
-
Hg19::chr1:246350393..246350413,-p@chr1:246350393..246350413
-
Hg19::chr1:3105351..3105356,-p@chr1:3105351..3105356
-
Hg19::chr2:105277766..105277771,+p@chr2:105277766..105277771
+
Hg19::chr4:54966328..54966335,+p1@GSX2
Hg19::chr4:57522753..57522760,-p18@HOPX
Hg19::chr4:96210568..96210572,+p@chr4:96210568..96210572
+
Hg19::chr7:142411990..142411991,+p@chr7:142411990..142411991
+
Hg19::chr7:1894156..1894165,-p@chr7:1894156..1894165
-
Hg19::chr7:26591452..26591463,+p1@ENST00000457000


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:0043416regulation of skeletal muscle regeneration0.00153655951960438
GO:0051153regulation of striated muscle cell differentiation0.00153655951960438
GO:0043415positive regulation of skeletal muscle regeneration0.00153655951960438
GO:0051149positive regulation of muscle cell differentiation0.00153655951960438
GO:0051155positive regulation of striated muscle cell differentiation0.00153655951960438
GO:0047961glycine N-acyltransferase activity0.00384105956936706
GO:0051147regulation of muscle cell differentiation0.00384105956936706
GO:0043403skeletal muscle regeneration0.00384105956936706
GO:0051146striated muscle cell differentiation0.012287049121659
GO:0042246tissue regeneration0.012287049121659
GO:0031099regeneration0.0125655603112768
GO:0043565sequence-specific DNA binding0.0140697158532347
GO:0048589developmental growth0.0218432594422842
GO:0042692muscle cell differentiation0.0240401833615157
GO:0045597positive regulation of cell differentiation0.0240401833615157
GO:0003700transcription factor activity0.0306706194259049
GO:0051094positive regulation of developmental process0.0306706194259049
GO:0014706striated muscle development0.0358946964492108
GO:0016410N-acyltransferase activity0.0358946964492108
GO:0007507heart development0.0360103844931409
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0455727226273163
GO:0042060wound healing0.0455727226273163
GO:0045595regulation of cell differentiation0.0475396809385267
GO:0007275multicellular organismal development0.0475396809385267



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell4.22e-08108
common myeloid progenitor4.22e-08108
Disease
Ontology termp-valuen
myeloid leukemia2.93e-2631
leukemia4.38e-2139
hematologic cancer2.36e-1651
immune system cancer2.36e-1651


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)
MA0003.10.000213103
MA0004.10.454064
MA0006.10.0632578
MA0007.10.137043
MA0009.14.37465
MA0014.18.83437e-05
MA0017.10.583727
MA0019.10.250001
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.0703882
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.620638
MA0040.10.440685
MA0041.12.14633
MA0042.11.98885
MA0043.10.510506
MA0046.10.500598
MA0048.10.00412155
MA0050.10.434675
MA0051.10.214141
MA0052.11.97408
MA0055.10.00634937
MA0056.10
MA0057.10.153032
MA0058.10.312452
MA0059.10.310646
MA0060.10.0226691
MA0061.10.193842
MA0063.10
MA0066.10.217443
MA0067.10.802392
MA0068.10.0481509
MA0069.10.497197
MA0070.11.2224
MA0071.11.67107
MA0072.10.483399
MA0073.10.0220979
MA0074.11.80069
MA0076.10.102323
MA0077.10.476645
MA0078.10.287843
MA0081.10.0933581
MA0083.10.516887
MA0084.10.981601
MA0087.10.481255
MA0088.10.00662157
MA0089.10
MA0090.10.110205
MA0091.10.895843
MA0092.10.127244
MA0093.10.497967
MA0095.10
MA0098.10
MA0100.10.227084
MA0101.10.0660267
MA0103.10.469617
MA0105.10.0169418
MA0106.10.247115
MA0107.10.0374129
MA0108.20.369058
MA0109.10
MA0111.10.375752
MA0113.10.259368
MA0114.10.600893
MA0115.10.730438
MA0116.10.151524
MA0117.10.543727
MA0119.10.0851434
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.302006
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.632521
MA0139.10.0139039
MA0140.10.551956
MA0141.10.637815
MA0142.10.913702
MA0143.10.7194
MA0144.10.554775
MA0145.10.00882108
MA0146.10.00423052
MA0147.10.356889
MA0148.10.164295
MA0149.10.18183
MA0062.20.0710269
MA0035.20.550801
MA0039.20.00297361
MA0138.20.288795
MA0002.21.02031
MA0137.20.543748
MA0104.20.241164
MA0047.20.238164
MA0112.20.00106228
MA0065.20.167354
MA0150.10.10696
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.10.39153
MA0155.10.00641934
MA0156.10.258514
MA0157.10.323429
MA0158.10
MA0159.10.358237
MA0160.10.99551
MA0161.10
MA0162.13.33344e-05
MA0163.10.000641122
MA0164.10.740687
MA0080.20.498167
MA0018.20.693153
MA0099.20.193081
MA0079.20.00162827
MA0102.21.01759
MA0258.10.524433
MA0259.10.374822
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
GATA2#262463.324764800057560.007322245068391930.0302838568310544



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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