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Coexpression cluster:C307: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.22599e-06,MA0004.1;0.0566508,MA0006.1;0.0696281,MA0007.1;0.418327,MA0009.1;0.332084,MA0014.1;6.8361e-07,MA0017.1;0.096641,MA0019.1;0.122811,MA0024.1;0.254518,MA0025.1;0.439186,MA0027.1;1.8466,MA0028.1;0.0801195,MA0029.1;2.08929,MA0030.1;0.720769,MA0031.1;0.215562,MA0038.1;0.673838,MA0040.1;0.749298,MA0041.1;0.492494,MA0042.1;1.15076,MA0043.1;0.332327,MA0046.1;0.323723,MA0048.1;0.170727,MA0050.1;0.19388,MA0051.1;0.32328,MA0052.1;0.275327,MA0055.1;0.556996,MA0056.1;0,MA0057.1;0.0869805,MA0058.1;0.0279236,MA0059.1;0.823005,MA0060.1;0.245358,MA0061.1;0.0376016,MA0063.1;0,MA0066.1;0.100184,MA0067.1;0.597968,MA0068.1;0.486581,MA0069.1;1.54815,MA0070.1;0.312273,MA0071.1;0.588101,MA0072.1;0.308875,MA0073.1;0.0126638,MA0074.1;0.322317,MA0076.1;0.306875,MA0077.1;0.303076,MA0078.1;0.45889,MA0081.1;0.515873,MA0083.1;0.337888,MA0084.1;0.768496,MA0087.1;0.307032,MA0088.1;0.145739,MA0089.1;0,MA0090.1;0.142663,MA0091.1;0.799469,MA0092.1;0.687103,MA0093.1;0.0154139,MA0095.1;0,MA0098.1;0,MA0100.1;0.705366,MA0101.1;0.372263,MA0103.1;0.169168,MA0105.1;0.0124597,MA0106.1;1.25559,MA0107.1;0.599065,MA0108.2;0.612085,MA0109.1;0,MA0111.1;0.356588,MA0113.1;0.406016,MA0114.1;0.205078,MA0115.1;0.530757,MA0116.1;0.103972,MA0117.1;0.36143,MA0119.1;0.102603,MA0122.1;0.382044,MA0124.1;2.14434,MA0125.1;0.42437,MA0130.1;0,MA0131.1;0.161082,MA0132.1;0,MA0133.1;0,MA0135.1;0.355725,MA0136.1;0.68982,MA0139.1;0.00855844,MA0140.1;2.6289,MA0141.1;0.113951,MA0142.1;0.567363,MA0143.1;0.129619,MA0144.1;0.52139,MA0145.1;0.0643794,MA0146.1;0.00539033,MA0147.1;0.107681,MA0148.1;0.0660128,MA0149.1;0.0768601,MA0062.2;0.0858982,MA0035.2;4.00579,MA0039.2;0.00403205,MA0138.2;0.151138,MA0002.2;2.09102,MA0137.2;0.411378,MA0104.2;0.0551645,MA0047.2;0.114453,MA0112.2;0.0268433,MA0065.2;0.927755,MA0150.1;0.321767,MA0151.1;0,MA0152.1;1.49249,MA0153.1;0.41053,MA0154.1;0.298544,MA0155.1;0.00310384,MA0156.1;0.68237,MA0157.1;0.177496,MA0158.1;0,MA0159.1;0.108362,MA0160.1;0.537314,MA0161.1;0,MA0162.1;0.00057372,MA0163.1;0.00586921,MA0164.1;1.35414,MA0080.2;0.606368,MA0018.2;0.385322,MA0099.2;0.0840507,MA0079.2;1.936e-09,MA0102.2;0.803155,MA0258.1;0.0235525,MA0259.1;0.0411886,MA0442.1;0
}}
}}

Revision as of 19:02, 22 January 2013


Full id: C307_acute_chronic_leukemia_CD133_Mast_CD34_anaplastic



Phase1 CAGE Peaks

Hg19::chr10:119134340..119134380,-p7@PDZD8
Hg19::chr10:63524374..63524382,-p@chr10:63524374..63524382
-
Hg19::chr10:63524394..63524413,-p@chr10:63524394..63524413
-
Hg19::chr10:63524414..63524429,-p@chr10:63524414..63524429
-
Hg19::chr10:63524522..63524527,-p@chr10:63524522..63524527
-
Hg19::chr10:73830184..73830199,-p16@SPOCK2
Hg19::chr10:73830227..73830232,-p26@SPOCK2
Hg19::chr12:10017724..10017738,-p@chr12:10017724..10017738
-
Hg19::chr12:11949422..11949423,-p@chr12:11949422..11949423
-
Hg19::chr12:11949500..11949512,-p@chr12:11949500..11949512
-
Hg19::chr12:27613673..27613722,-p@chr12:27613673..27613722
-
Hg19::chr12:54784375..54784386,-p@chr12:54784375..54784386
-
Hg19::chr15:82336577..82336584,-p14@MEX3B
Hg19::chr15:82336770..82336786,-p11@MEX3B
Hg19::chr15:82336795..82336817,-p5@MEX3B
Hg19::chr17:17140639..17140672,-p2@FLCN
p3@PLD6
Hg19::chr19:14590350..14590358,-p@chr19:14590350..14590358
-
Hg19::chr1:237957220..237957263,+p@chr1:237957220..237957263
+
Hg19::chr22:30138461..30138492,-p@chr22:30138461..30138492
-
Hg19::chr2:197674076..197674085,-p@chr2:197674076..197674085
-
Hg19::chr2:98375925..98375935,-p17@TMEM131
Hg19::chr3:126937310..126937322,-p@chr3:126937310..126937322
-
Hg19::chr3:126937399..126937417,-p@chr3:126937399..126937417
-
Hg19::chr5:134696315..134696329,-p@chr5:134696315..134696329
-
Hg19::chr5:134696342..134696362,-p@chr5:134696342..134696362
-
Hg19::chr5:178996177..178996199,+p@chr5:178996177..178996199
+
Hg19::chr5:178996248..178996252,+p@chr5:178996248..178996252
+
Hg19::chr5:178996255..178996266,+p@chr5:178996255..178996266
+
Hg19::chr5:178996286..178996298,+p@chr5:178996286..178996298
+
Hg19::chr5:178996302..178996310,+p@chr5:178996302..178996310
+
Hg19::chr5:53606258..53606271,-p5@ARL15
Hg19::chr5:53606272..53606277,-p6@ARL15
Hg19::chr8:62597218..62597226,-p27@ASPH
Hg19::chr8:62597251..62597256,-p29@ASPH
Hg19::chr9:22922267..22922278,-p@chr9:22922267..22922278
-
Hg19::chrX:155227315..155227335,+p3@IL9R
Hg19::chrX:155227354..155227366,+p1@IL9R
Hg19::chrX:155227375..155227392,+p2@IL9R
Hg19::chrX:15589921..15589927,-p@chrX:15589921..15589927
-


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:0019983interleukin-9 binding0.0143647709878724
GO:0004919interleukin-9 receptor activity0.0143647709878724



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 cell1.03e-09108
common myeloid progenitor1.03e-09108
Disease
Ontology termp-valuen
chronic leukemia9.20e-458
acute myeloid leukemia6.62e-411
myeloid leukemia2.26e-3231
leukemia6.58e-2639
hematologic cancer5.31e-2051
immune system cancer5.31e-2051
organ system cancer8.63e-08137


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)
MA0003.11.22599e-06
MA0004.10.0566508
MA0006.10.0696281
MA0007.10.418327
MA0009.10.332084
MA0014.16.8361e-07
MA0017.10.096641
MA0019.10.122811
MA0024.10.254518
MA0025.10.439186
MA0027.11.8466
MA0028.10.0801195
MA0029.12.08929
MA0030.10.720769
MA0031.10.215562
MA0038.10.673838
MA0040.10.749298
MA0041.10.492494
MA0042.11.15076
MA0043.10.332327
MA0046.10.323723
MA0048.10.170727
MA0050.10.19388
MA0051.10.32328
MA0052.10.275327
MA0055.10.556996
MA0056.10
MA0057.10.0869805
MA0058.10.0279236
MA0059.10.823005
MA0060.10.245358
MA0061.10.0376016
MA0063.10
MA0066.10.100184
MA0067.10.597968
MA0068.10.486581
MA0069.11.54815
MA0070.10.312273
MA0071.10.588101
MA0072.10.308875
MA0073.10.0126638
MA0074.10.322317
MA0076.10.306875
MA0077.10.303076
MA0078.10.45889
MA0081.10.515873
MA0083.10.337888
MA0084.10.768496
MA0087.10.307032
MA0088.10.145739
MA0089.10
MA0090.10.142663
MA0091.10.799469
MA0092.10.687103
MA0093.10.0154139
MA0095.10
MA0098.10
MA0100.10.705366
MA0101.10.372263
MA0103.10.169168
MA0105.10.0124597
MA0106.11.25559
MA0107.10.599065
MA0108.20.612085
MA0109.10
MA0111.10.356588
MA0113.10.406016
MA0114.10.205078
MA0115.10.530757
MA0116.10.103972
MA0117.10.36143
MA0119.10.102603
MA0122.10.382044
MA0124.12.14434
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.355725
MA0136.10.68982
MA0139.10.00855844
MA0140.12.6289
MA0141.10.113951
MA0142.10.567363
MA0143.10.129619
MA0144.10.52139
MA0145.10.0643794
MA0146.10.00539033
MA0147.10.107681
MA0148.10.0660128
MA0149.10.0768601
MA0062.20.0858982
MA0035.24.00579
MA0039.20.00403205
MA0138.20.151138
MA0002.22.09102
MA0137.20.411378
MA0104.20.0551645
MA0047.20.114453
MA0112.20.0268433
MA0065.20.927755
MA0150.10.321767
MA0151.10
MA0152.11.49249
MA0153.10.41053
MA0154.10.298544
MA0155.10.00310384
MA0156.10.68237
MA0157.10.177496
MA0158.10
MA0159.10.108362
MA0160.10.537314
MA0161.10
MA0162.10.00057372
MA0163.10.00586921
MA0164.11.35414
MA0080.20.606368
MA0018.20.385322
MA0099.20.0840507
MA0079.21.936e-09
MA0102.20.803155
MA0258.10.0235525
MA0259.10.0411886
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#262482.614344970985430.009741185919473360.0366325693592063



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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