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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C212_chronic_acute_Whole_Reticulocytes_leukemia_blood_CD34
|full_id=C212_chronic_acute_Whole_Reticulocytes_leukemia_blood_CD34
|id=C212
|id=C212

Revision as of 14:48, 12 September 2012


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>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism7.18e-36115
neural tube3.75e-1357
neural rod3.75e-1357
future spinal cord3.75e-1357
neural keel3.75e-1357
central nervous system6.66e-1282
anterior neural tube7.39e-1242
regional part of forebrain1.65e-1141
forebrain1.65e-1141
future forebrain1.65e-1141
regional part of nervous system1.87e-1194
nervous system1.87e-1194
telencephalon6.86e-1134
gray matter8.94e-1134
brain grey matter8.94e-1134
regional part of brain1.51e-1059
regional part of telencephalon1.94e-1033
regional part of cerebral cortex2.91e-1022
brain3.11e-1069
future brain3.11e-1069
cerebral hemisphere3.41e-1032
neocortex1.56e-0920
cerebral cortex9.07e-0925
pallium9.07e-0925
neurectoderm1.72e-0890
neural plate1.86e-0886
presumptive neural plate1.86e-0886
blood2.16e-0815
haemolymphatic fluid2.16e-0815
organism substance2.16e-0815
Disease
Ontology termp-valuen
leukemia6.05e-1839
hematologic cancer6.23e-1651
immune system cancer6.23e-1651
myeloid leukemia1.07e-1531
chronic leukemia7.87e-078


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)

{{{tfbs_overrepresentation_jaspar}}}



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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