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

Latest revision as of 10:57, 17 September 2013


Full id: C212_chronic_acute_Whole_Reticulocytes_leukemia_blood_CD34



Phase1 CAGE Peaks

Hg19::chr11:129815255..129815259,-p@chr11:129815255..129815259
-
Hg19::chr11:36119803..36119812,+p6@LDLRAD3
Hg19::chr11:36119821..36119838,+p3@LDLRAD3
Hg19::chr11:36119843..36119865,+p2@LDLRAD3
Hg19::chr11:36119875..36119897,+p4@LDLRAD3
Hg19::chr11:36119908..36119916,+p7@LDLRAD3
Hg19::chr11:59875891..59875903,-p@chr11:59875891..59875903
-
Hg19::chr11:66469231..66469245,-p@chr11:66469231..66469245
-
Hg19::chr11:66469256..66469259,-p@chr11:66469256..66469259
-
Hg19::chr11:66469260..66469272,-p@chr11:66469260..66469272
-
Hg19::chr13:109281940..109281948,+p11@MYO16
Hg19::chr13:109281953..109281967,+p1@MYO16
Hg19::chr13:109281972..109281975,+p16@MYO16
Hg19::chr13:109281990..109282005,+p2@MYO16
Hg19::chr13:109282019..109282027,+p9@MYO16
Hg19::chr13:114770418..114770438,-p@chr13:114770418..114770438
-
Hg19::chr13:52568084..52568091,-p@chr13:52568084..52568091
-
Hg19::chr14:81894113..81894122,-p5@STON2
Hg19::chr16:2007750..2007753,-p@chr16:2007750..2007753
-
Hg19::chr17:42466942..42466947,-p6@ITGA2B
Hg19::chr18:24283586..24283611,-p1@LOC728606
Hg19::chr18:24283637..24283652,-p2@LOC728606
Hg19::chr19:16011113..16011119,+p@chr19:16011113..16011119
+
Hg19::chr1:147144518..147144523,+p@chr1:147144518..147144523
+
Hg19::chr1:182750217..182750222,-p@chr1:182750217..182750222
-
Hg19::chr1:236205360..236205375,-p@chr1:236205360..236205375
-
Hg19::chr1:246588665..246588670,+p@chr1:246588665..246588670
+
Hg19::chr20:11562510..11562525,-p@chr20:11562510..11562525
-
Hg19::chr20:40344270..40344278,-p@chr20:40344270..40344278
-
Hg19::chr21:16125888..16125904,-p2@ENST00000454128
Hg19::chr22:48134043..48134048,+p@chr22:48134043..48134048
+
Hg19::chr2:159992199..159992211,+p9@TANC1
Hg19::chr2:159994630..159994641,+p@chr2:159994630..159994641
+
Hg19::chr2:190448096..190448099,-p15@SLC40A1
Hg19::chr2:190448106..190448113,-p14@SLC40A1
Hg19::chr2:190448118..190448135,-p4@SLC40A1
Hg19::chr2:209436695..209436715,+p@chr2:209436695..209436715
+
Hg19::chr4:101801270..101801292,-p8@EMCN
Hg19::chr4:103266004..103266021,-p8@SLC39A8
Hg19::chr4:139694701..139694704,+p1@ENST00000502606
Hg19::chr4:139694723..139694753,+p1@ENST00000513400
Hg19::chr4:158656484..158656489,+p@chr4:158656484..158656489
+
Hg19::chr5:134812596..134812620,+p@chr5:134812596..134812620
+
Hg19::chr5:3778511..3778555,+p@chr5:3778511..3778555
+
Hg19::chr5:3784749..3784775,+p@chr5:3784749..3784775
+
Hg19::chr6:124401262..124401310,+p@chr6:124401262..124401310
+
Hg19::chr6:136687033..136687059,-p@chr6:136687033..136687059
-
Hg19::chr6:156941231..156941245,-p@chr6:156941231..156941245
-
Hg19::chr6:16317123..16317126,+p@chr6:16317123..16317126
+
Hg19::chr6:83604219..83604223,+p@chr6:83604219..83604223
+
Hg19::chr7:150654775..150654789,-p@chr7:150654775..150654789
-
Hg19::chr7:150657066..150657083,-p@chr7:150657066..150657083
-
Hg19::chr7:150657124..150657149,-p@chr7:150657124..150657149
-
Hg19::chr7:24835099..24835127,-p@chr7:24835099..24835127
-
Hg19::chr8:105683304..105683308,+p@chr8:105683304..105683308
+
Hg19::chr8:141312919..141312935,-p8@TRAPPC9
Hg19::chr8:28402477..28402490,-p@chr8:28402477..28402490
-
Hg19::chr8:50219668..50219674,+p@chr8:50219668..50219674
+
Hg19::chr8:86240792..86240832,+p1@CU693313
Hg19::chr8:86245780..86245790,-p@chr8:86245780..86245790
-
Hg19::chr8:86290333..86290348,-p1@CA1
Hg19::chr8:91233711..91233743,+p1@ENST00000517400
p1@ENST00000523283
Hg19::chr8:91233744..91233747,+p1@ENST00000524361
Hg19::chr8:91233750..91233766,+p1@ENST00000523406
Hg19::chr8:91233779..91233788,+p3@ENST00000523406
Hg19::chr8:91233817..91233828,+p2@ENST00000523406
Hg19::chr8:91411865..91411868,+p@chr8:91411865..91411868
+
Hg19::chrX:113302371..113302387,-p@chrX:113302371..113302387
-
Hg19::chrX:135866631..135866640,+p@chrX:135866631..135866640
+
Hg19::chrX:81069119..81069129,+p@chrX:81069119..81069129
+


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

No GOStat results

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 myeloid leukemia9.91e-411
myeloid leukemia2.26e-3231
leukemia6.58e-2639
chronic leukemia7.35e-218
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)
MA0003.17.13602e-15
MA0004.10.28342
MA0006.10.00707961
MA0007.10.435494
MA0009.10.980745
MA0014.12.55468e-07
MA0017.10.205139
MA0019.10.955394
MA0024.10.114848
MA0025.11.30887
MA0027.11.59503
MA0028.10.00134145
MA0029.13.99271
MA0030.10.118668
MA0031.10.29941
MA0038.10.499316
MA0040.10.400295
MA0041.10.0593568
MA0042.10.0446767
MA0043.10.509267
MA0046.11.52294
MA0048.10.000176936
MA0050.10.260887
MA0051.10.107443
MA0052.10.80628
MA0055.10.00218508
MA0056.10
MA0057.10.00052021
MA0058.10.0585351
MA0059.10.415149
MA0060.10.889227
MA0061.10.173259
MA0063.10
MA0066.10.801584
MA0067.10.390744
MA0068.10.00422002
MA0069.10.946021
MA0070.11.4728
MA0071.10.411679
MA0072.10.466227
MA0073.15.19869e-13
MA0074.10.106914
MA0076.10.00376954
MA0077.10.149129
MA0078.10.189352
MA0081.10.252203
MA0083.13.00678
MA0084.10.545308
MA0087.10.152017
MA0088.10.0498285
MA0089.10
MA0090.10.0797925
MA0091.10.0104011
MA0092.10.222398
MA0093.10.0701154
MA0095.10
MA0098.10
MA0100.10.120599
MA0101.10.261151
MA0103.10.125613
MA0105.10.0132555
MA0106.10.0356382
MA0107.10.197713
MA0108.20.295867
MA0109.10
MA0111.10.0905593
MA0113.10.0399161
MA0114.10.0227064
MA0115.10.332087
MA0116.10.061421
MA0117.10.193003
MA0119.11.37743
MA0122.10.209091
MA0124.10.301544
MA0125.11.26357
MA0130.10
MA0131.10.206843
MA0132.10
MA0133.10
MA0135.11.0533
MA0136.10.278172
MA0139.10.000782521
MA0140.111.3178
MA0141.10.131363
MA0142.10.558185
MA0143.11.42486
MA0144.10.249143
MA0145.10.00148882
MA0146.11.37536e-08
MA0147.10.0647339
MA0148.10.0625861
MA0149.10.0169186
MA0062.20.0109991
MA0035.210.4593
MA0039.22.17184e-06
MA0138.20.0511211
MA0002.20.611953
MA0137.20.468293
MA0104.20.0231781
MA0047.20.0326619
MA0112.20.00256483
MA0065.20.00411827
MA0150.10.307399
MA0151.10
MA0152.11.39773
MA0153.10.655013
MA0154.10.404306
MA0155.10.0164268
MA0156.10.179316
MA0157.10.505035
MA0158.10
MA0159.10.000266135
MA0160.10.361491
MA0161.10
MA0162.14.3251e-09
MA0163.14.443e-06
MA0164.11.97795
MA0080.20.586562
MA0018.20.0359876
MA0099.20.21979
MA0079.20
MA0102.20.577493
MA0258.10.135114
MA0259.10.139731
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
GATA1#2623214.068092443140131.80943924759705e-081.30328293503302e-06
GATA2#2624274.915902240085118.77578425512912e-131.23855963759653e-10
REST#5978141.93000574322560.01178303923400240.0429322088529156
SMARCA4#659748.95805161759360.001081382885241040.00763304590103332
TAL1#68862711.52075214701276.25039865498278e-221.72694546330092e-19



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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