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Coexpression cluster:C1390: Difference between revisions

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{{Coexpression_clusters
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sequestering of NF-kappaB!0.0120973193800372!9908$GO:0042347!negative regulation of NF-kappaB import into nucleus!0.0120973193800372!9908$GO:0000242!pericentriolar material!0.0120973193800372!5108$GO:0042994!cytoplasmic sequestering of transcription factor!0.0120973193800372!9908$GO:0051220!cytoplasmic sequestering of protein!0.0120973193800372!9908$GO:0042308!negative regulation of protein import into nucleus!0.0120973193800372!9908$GO:0042992!negative regulation of transcription factor import into nucleus!0.0120973193800372!9908$GO:0042345!regulation of NF-kappaB import into nucleus!0.0120973193800372!9908$GO:0042348!NF-kappaB import into nucleus!0.0120973193800372!9908$GO:0046823!negative regulation of nucleocytoplasmic transport!0.0120973193800372!9908$GO:0051224!negative regulation of protein transport!0.0120973193800372!9908$GO:0030159!receptor signaling complex scaffold activity!0.0120973193800372!9908$GO:0032947!protein complex scaffold!0.0120973193800372!9908$GO:0042990!regulation of transcription factor import into nucleus!0.0120973193800372!9908$GO:0042991!transcription factor import into nucleus!0.0120973193800372!9908$GO:0033157!regulation of intracellular protein transport!0.0120973193800372!9908$GO:0042306!regulation of protein import into nucleus!0.0120973193800372!9908$GO:0044450!microtubule organizing center part!0.0120973193800372!5108$GO:0032507!maintenance of cellular protein localization!0.0120973193800372!9908$GO:0051651!maintenance of cellular localization!0.0120973193800372!9908$GO:0032386!regulation of intracellular transport!0.0120973193800372!9908$GO:0045185!maintenance of protein localization!0.0120973193800372!9908$GO:0051223!regulation of protein transport!0.012367641059904!9908$GO:0046822!regulation of nucleocytoplasmic transport!0.012367641059904!9908$GO:0051051!negative regulation of transport!0.0126910111404423!9908$GO:0048523!negative regulation of cellular process!0.0146464428917892!9908;1810$GO:0048519!negative regulation of biological process!0.0149820926239023!9908;1810$GO:0051235!maintenance of localization!0.0149820926239023!9908$GO:0051028!mRNA transport!0.0284818448587953!9908$GO:0050658!RNA transport!0.0284818448587953!9908$GO:0051236!establishment of RNA localization!0.0284818448587953!9908$GO:0050657!nucleic acid transport!0.0284818448587953!9908$GO:0006403!RNA localization!0.0284818448587953!9908$GO:0006606!protein import into nucleus!0.0286006223338466!9908$GO:0051170!nuclear import!0.0286006223338466!9908$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0295033620528052!9908$GO:0003714!transcription corepressor activity!0.0295314200752571!1810$GO:0051049!regulation of transport!0.0295578589690544!9908$GO:0017038!protein import!0.0319304854904982!9908$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.032108983109937!1810$GO:0005813!centrosome!0.032108983109937!5108$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.0337643347359911!9908$GO:0005815!microtubule organizing center!0.0348689724031423!5108$GO:0006913!nucleocytoplasmic transport!0.0353498133259162!9908$GO:0051169!nuclear transport!0.0353498133259162!9908$GO:0045892!negative regulation of transcription, DNA-dependent!0.0449377503640029!1810$GO:0005515!protein binding!0.0452836447329336!9908;5108;1810$GO:0016564!transcription repressor activity!0.0452836447329336!1810$GO:0006605!protein 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810597,MA0158.1;0,MA0159.1;0.875329,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.347838,MA0163.1;0.813808,MA0164.1;0.738243,MA0080.2;1.02158,MA0018.2;1.69036,MA0099.2;0.629739,MA0079.2;0.35176,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.893594,MA0442.1;0}}
|full_id=C1390_Mast_CD8_Natural_Basophils_CD34_CD4_CD19
|id=C1390
}}

Latest revision as of 11:43, 17 September 2013


Full id: C1390_Mast_CD8_Natural_Basophils_CD34_CD4_CD19



Phase1 CAGE Peaks

Hg19::chr14:23025207..23025219,-p@chr14:23025207..23025219
-
Hg19::chr17:7743554..7743563,+p@chr17:7743554..7743563
+
Hg19::chr1:67519625..67519640,-p1@AB385301
Hg19::chr1:93812261..93812303,+p2@DR1
Hg19::chr4:76598434..76598445,-p6@G3BP2
Hg19::chr8:17780648..17780659,+p4@PCM1


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:0007253cytoplasmic sequestering of NF-kappaB0.0120973193800372
GO:0042347negative regulation of NF-kappaB import into nucleus0.0120973193800372
GO:0000242pericentriolar material0.0120973193800372
GO:0042994cytoplasmic sequestering of transcription factor0.0120973193800372
GO:0051220cytoplasmic sequestering of protein0.0120973193800372
GO:0042308negative regulation of protein import into nucleus0.0120973193800372
GO:0042992negative regulation of transcription factor import into nucleus0.0120973193800372
GO:0042345regulation of NF-kappaB import into nucleus0.0120973193800372
GO:0042348NF-kappaB import into nucleus0.0120973193800372
GO:0046823negative regulation of nucleocytoplasmic transport0.0120973193800372
GO:0051224negative regulation of protein transport0.0120973193800372
GO:0030159receptor signaling complex scaffold activity0.0120973193800372
GO:0032947protein complex scaffold0.0120973193800372
GO:0042990regulation of transcription factor import into nucleus0.0120973193800372
GO:0042991transcription factor import into nucleus0.0120973193800372
GO:0033157regulation of intracellular protein transport0.0120973193800372
GO:0042306regulation of protein import into nucleus0.0120973193800372
GO:0044450microtubule organizing center part0.0120973193800372
GO:0032507maintenance of cellular protein localization0.0120973193800372
GO:0051651maintenance of cellular localization0.0120973193800372
GO:0032386regulation of intracellular transport0.0120973193800372
GO:0045185maintenance of protein localization0.0120973193800372
GO:0051223regulation of protein transport0.012367641059904
GO:0046822regulation of nucleocytoplasmic transport0.012367641059904
GO:0051051negative regulation of transport0.0126910111404423
GO:0048523negative regulation of cellular process0.0146464428917892
GO:0048519negative regulation of biological process0.0149820926239023
GO:0051235maintenance of localization0.0149820926239023
GO:0051028mRNA transport0.0284818448587953
GO:0050658RNA transport0.0284818448587953
GO:0051236establishment of RNA localization0.0284818448587953
GO:0050657nucleic acid transport0.0284818448587953
GO:0006403RNA localization0.0284818448587953
GO:0006606protein import into nucleus0.0286006223338466
GO:0051170nuclear import0.0286006223338466
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0295033620528052
GO:0003714transcription corepressor activity0.0295314200752571
GO:0051049regulation of transport0.0295578589690544
GO:0017038protein import0.0319304854904982
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.032108983109937
GO:0005813centrosome0.032108983109937
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0337643347359911
GO:0005815microtubule organizing center0.0348689724031423
GO:0006913nucleocytoplasmic transport0.0353498133259162
GO:0051169nuclear transport0.0353498133259162
GO:0045892negative regulation of transcription, DNA-dependent0.0449377503640029
GO:0005515protein binding0.0452836447329336
GO:0016564transcription repressor activity0.0452836447329336
GO:0006605protein targeting0.0452836447329336



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><br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.47e-29168
angioblastic mesenchymal cell1.47e-29168
hematopoietic cell7.74e-28177
leukocyte9.25e-28136
hematopoietic oligopotent progenitor cell6.55e-26161
hematopoietic multipotent progenitor cell6.55e-26161
hematopoietic lineage restricted progenitor cell3.96e-22120
nongranular leukocyte8.16e-21115
mesenchymal cell1.58e-13354
lymphocyte2.30e-1353
common lymphoid progenitor2.30e-1353
connective tissue cell4.93e-13361
lymphoid lineage restricted progenitor cell5.53e-1352
nucleate cell6.01e-1355
myeloid cell6.83e-13108
common myeloid progenitor6.83e-13108
motile cell9.39e-12386
myeloid leukocyte9.74e-1172
granulocyte monocyte progenitor cell5.11e-1067
stem cell8.73e-10441
multi fate stem cell2.68e-09427
myeloid lineage restricted progenitor cell5.27e-0966
somatic stem cell1.47e-08433
T cell4.63e-0825
pro-T cell4.63e-0825
macrophage dendritic cell progenitor4.76e-0861
monopoietic cell3.30e-0759
monocyte3.30e-0759
monoblast3.30e-0759
promonocyte3.30e-0759
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.63e-1598
blood island2.63e-1598
hemolymphoid system2.80e-12108
connective tissue7.75e-12371
blood4.04e-0915
haemolymphatic fluid4.04e-0915
organism substance4.04e-0915
bone marrow7.29e-0876
immune system4.06e-0793
bone element6.83e-0782
skeletal system9.30e-07100


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)
MA0003.10.515118
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.12.99917
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.11.62836
MA0101.10.397846
MA0103.10.381434
MA0105.11.34409
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.232472
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.680553
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.813808
MA0164.10.738243
MA0080.21.02158
MA0018.21.69036
MA0099.20.629739
MA0079.20.35176
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
BCL3#602211.51570093457940.01162725346801640.0424787044791744
GATA1#262336.780154071900220.006765763983348560.0287496795775466
GATA2#262436.3724658667770.008058821308742550.0318881275541321
SP1#666743.79892091876060.01052246616798510.0389452067516547
SREBF1#6720215.66861648016280.006411283165809460.0278902033719583
USF2#739236.49609869253480.007634319815300560.0314562167984446



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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