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Coexpression cluster:C1115: Difference between revisions

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{{Coexpression_clusters
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regulation of mRNA 3'-end processing!0.00520005491694157!4686$GO:0050685!positive regulation of mRNA processing!0.00520005491694157!4686$GO:0004294!tripeptidyl-peptidase II activity!0.00520005491694157!7174$GO:0008717!D-alanyl-D-alanine endopeptidase activity!0.00520005491694157!7174$GO:0031974!membrane-enclosed lumen!0.00520005491694157!152926;80314;4686$GO:0043233!organelle lumen!0.00520005491694157!152926;80314;4686$GO:0051254!positive regulation of RNA metabolic process!0.00520005491694157!4686$GO:0008240!tripeptidyl-peptidase activity!0.00520005491694157!7174$GO:0031440!regulation of mRNA 3'-end processing!0.00520005491694157!4686$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0112746726374699!80314;4686$GO:0000339!RNA cap binding!0.0133668470752712!4686$GO:0031325!positive regulation of cellular metabolic process!0.0133668470752712!80314;4686$GO:0006379!mRNA cleavage!0.0133668470752712!4686$GO:0050684!regulation of mRNA processing!0.0133668470752712!4686$GO:0009893!positive regulation of metabolic process!0.0136880817127755!80314;4686$GO:0031124!mRNA 3'-end processing!0.0204607554870117!4686$GO:0005654!nucleoplasm!0.0211322557389912!80314;4686$GO:0031123!RNA 3'-end processing!0.0233768379318203!4686$GO:0051252!regulation of RNA metabolic process!0.0233768379318203!4686$GO:0006406!mRNA export from nucleus!0.025709980262606!4686$GO:0043170!macromolecule metabolic process!0.0273417798653032!152926;80314;80063;4686;7174$GO:0045814!negative regulation of gene expression, epigenetic!0.0273417798653032!80314$GO:0031981!nuclear lumen!0.0273417798653032!80314;4686$GO:0006405!RNA export from nucleus!0.0292021291118577!4686$GO:0004289!subtilase activity!0.0323355491475181!7174$GO:0015071!protein phosphatase type 2C activity!0.0323355491475181!152926$GO:0051168!nuclear export!0.0380395566131108!4686$GO:0044237!cellular metabolic process!0.0396635721962796!152926;80314;80063;4686;7174$GO:0048522!positive regulation of cellular process!0.0396635721962796!80314;4686$GO:0044238!primary metabolic process!0.0396635721962796!152926;80314;80063;4686;7174$GO:0044424!intracellular part!0.0413916159462054!152926;80314;80063;4686;7174$GO:0008287!protein serine/threonine phosphatase complex!0.0415469369327996!152926$GO:0048518!positive regulation of biological process!0.0432967094918313!80314;4686$GO:0040029!regulation of gene expression, epigenetic!0.0432967094918313!80314$GO:0004722!protein serine/threonine phosphatase activity!0.0432967094918313!152926$GO:0044428!nuclear part!0.043958325953636!80314;4686$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0472815342760447!80314;80063;4686$GO:0051028!mRNA transport!0.0475876790435889!4686$GO:0043283!biopolymer metabolic process!0.0475876790435889!152926;80314;80063;4686$GO:0004177!aminopeptidase activity!0.0475876790435889!7174$GO:0031323!regulation of cellular metabolic process!0.0475876790435889!80314;80063;4686$GO:0050658!RNA transport!0.0475876790435889!4686$GO:0051236!establishment of RNA localization!0.0475876790435889!4686$GO:0050657!nucleic acid transport!0.0475876790435889!4686$GO:0006403!RNA localization!0.0475876790435889!4686$GO:0044446!intracellular organelle part!0.0483810973952469!152926;80314;4686$GO:0044422!organelle part!0.0483810973952469!152926;80314;4686$GO:0019222!regulation of metabolic process!0.0483810973952469!80314;80063;4686$GO:0016070!RNA metabolic process!0.0483810973952469!80314;80063;4686$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid 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|full_id=C1115_CD4_CD34_CD8_CD19_Basophils_Peripheral_Dendritic
|id=C1115
}}

Latest revision as of 11:38, 17 September 2013


Full id: C1115_CD4_CD34_CD8_CD19_Basophils_Peripheral_Dendritic



Phase1 CAGE Peaks

Hg19::chr10:32667648..32667659,-p5@EPC1
Hg19::chr10:32667660..32667735,-p2@EPC1
Hg19::chr13:103249302..103249321,+p2@TPP2
Hg19::chr16:10479876..10479887,+p2@ATF7IP2
Hg19::chr2:242823508..242823531,+p1@ENST00000415434
p1@ENST00000430555
p1@ENST00000457686
Hg19::chr4:89205879..89205911,-p3@PPM1K
Hg19::chr9:100396030..100396055,+p3@NCBP1


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:0031442positive regulation of mRNA 3'-end processing0.00520005491694157
GO:0050685positive regulation of mRNA processing0.00520005491694157
GO:0004294tripeptidyl-peptidase II activity0.00520005491694157
GO:0008717D-alanyl-D-alanine endopeptidase activity0.00520005491694157
GO:0031974membrane-enclosed lumen0.00520005491694157
GO:0043233organelle lumen0.00520005491694157
GO:0051254positive regulation of RNA metabolic process0.00520005491694157
GO:0008240tripeptidyl-peptidase activity0.00520005491694157
GO:0031440regulation of mRNA 3'-end processing0.00520005491694157
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0112746726374699
GO:0000339RNA cap binding0.0133668470752712
GO:0031325positive regulation of cellular metabolic process0.0133668470752712
GO:0006379mRNA cleavage0.0133668470752712
GO:0050684regulation of mRNA processing0.0133668470752712
GO:0009893positive regulation of metabolic process0.0136880817127755
GO:0031124mRNA 3'-end processing0.0204607554870117
GO:0005654nucleoplasm0.0211322557389912
GO:0031123RNA 3'-end processing0.0233768379318203
GO:0051252regulation of RNA metabolic process0.0233768379318203
GO:0006406mRNA export from nucleus0.025709980262606
GO:0043170macromolecule metabolic process0.0273417798653032
GO:0045814negative regulation of gene expression, epigenetic0.0273417798653032
GO:0031981nuclear lumen0.0273417798653032
GO:0006405RNA export from nucleus0.0292021291118577
GO:0004289subtilase activity0.0323355491475181
GO:0015071protein phosphatase type 2C activity0.0323355491475181
GO:0051168nuclear export0.0380395566131108
GO:0044237cellular metabolic process0.0396635721962796
GO:0048522positive regulation of cellular process0.0396635721962796
GO:0044238primary metabolic process0.0396635721962796
GO:0044424intracellular part0.0413916159462054
GO:0008287protein serine/threonine phosphatase complex0.0415469369327996
GO:0048518positive regulation of biological process0.0432967094918313
GO:0040029regulation of gene expression, epigenetic0.0432967094918313
GO:0004722protein serine/threonine phosphatase activity0.0432967094918313
GO:0044428nuclear part0.043958325953636
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0472815342760447
GO:0051028mRNA transport0.0475876790435889
GO:0043283biopolymer metabolic process0.0475876790435889
GO:0004177aminopeptidase activity0.0475876790435889
GO:0031323regulation of cellular metabolic process0.0475876790435889
GO:0050658RNA transport0.0475876790435889
GO:0051236establishment of RNA localization0.0475876790435889
GO:0050657nucleic acid transport0.0475876790435889
GO:0006403RNA localization0.0475876790435889
GO:0044446intracellular organelle part0.0483810973952469
GO:0044422organelle part0.0483810973952469
GO:0019222regulation of metabolic process0.0483810973952469
GO:0016070RNA metabolic process0.0483810973952469
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0483810973952469



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 organism2.92e-24114
neural tube1.45e-1456
neural rod1.45e-1456
future spinal cord1.45e-1456
neural keel1.45e-1456
regional part of nervous system8.03e-1453
regional part of brain8.03e-1453
nervous system1.58e-1389
central nervous system5.09e-1381
regional part of forebrain6.11e-1341
forebrain6.11e-1341
anterior neural tube6.11e-1341
future forebrain6.11e-1341
brain1.05e-1168
future brain1.05e-1168
telencephalon1.49e-1034
brain grey matter1.55e-1034
gray matter1.55e-1034
cerebral hemisphere1.94e-1032
regional part of telencephalon2.90e-1032
neurectoderm1.39e-0886
regional part of cerebral cortex2.03e-0822
cerebral cortex3.60e-0825
pallium3.60e-0825
neocortex6.66e-0820
neural plate8.32e-0882
presumptive neural plate8.32e-0882
blood1.73e-0715
haemolymphatic fluid1.73e-0715
organism substance1.73e-0715
Disease
Ontology termp-valuen
hematologic cancer2.51e-0751
immune system cancer2.51e-0751


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)
MA0003.11.35295
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.12.01466
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.11.47594
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.744639
MA0058.11.04727
MA0059.10.404929
MA0060.12.61656
MA0061.11.71672
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.11.11391
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.11.64331
MA0103.10.332048
MA0105.12.29445
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.11.59899
MA0144.10.254954
MA0145.10.581146
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.60756
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.11.72058
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.361922
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
CHD2#110657.38858773865490.0001498689600820670.00193141218188685
E2F1#186953.505278010628090.005090553587915050.0236837280010807
E2F4#187435.429168706550470.01350675082176140.0477032075030923
EGR1#195853.562985067721530.004722351211058930.0222552068106937
ELF1#199753.041498542005380.009719562269370750.0365565169926106
EP300#203343.870823843556110.01142567586684480.041859408631473
FOS#235345.141688747939660.004042095865678250.0193479284163147
GTF2B#2959418.25361710532813.11241110089347e-050.0006292239701243
GTF2F1#296235.459854661467560.0132988216841570.0470213161985129
HEY1#2346263.462952322662040.001267890095872120.00850354313657776
IRF1#365944.364093573465090.00739345582427820.0305493405931236
NANOG#79923312.53347649186260.001261052189503470.00846747007969353
NFKB1#479053.92004530299560.003036581424484610.0161155306363
NFYA#4800615.7933548855691.7032585757508e-079.38220582240704e-06
NFYB#4801614.36553707445982.99325254948281e-071.50947514734638e-05
PAX5#507943.811180303530190.01208261681555190.0438204124596112
POLR2A#543072.147453176558070.004747636447610280.0223219917594188
REST#597856.892877654377160.0002094388584846510.00243825492601477
RFX5#5993610.32678070902442.12421369818918e-067.73538195345816e-05
SP1#666764.884326895549340.0001736361122290910.00211282557673238
SP2#6668414.94487456791126.81071539656055e-050.00108762126192873
TAF1#687262.865468244924540.003728330207471460.0185818696510671
TBP#690863.177232017511190.002074112051852660.0120149863322114
TCF7L2#693446.154386607507050.002064676148138040.0119689560521419
TRIM28#1015537.967367876541080.004622341263156460.0218311716719937
YY1#752853.507979107038470.005072570672808980.0236095284325281



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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