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Coexpression cluster:C2054: Difference between revisions

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{{Coexpression_clusters
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dendritic cell differentiation!0.0085925308502013!5971$GO:0001773!myeloid dendritic cell activation!0.0085925308502013!5971$GO:0045063!T-helper 1 cell differentiation!0.0085925308502013!5971$GO:0042994!cytoplasmic sequestering of transcription factor!0.0085925308502013!4794$GO:0002294!CD4-positive, alpha-beta T cell differentiation during immune response!0.0085925308502013!5971$GO:0002292!T cell differentiation during immune response!0.0085925308502013!5971$GO:0042093!T-helper cell differentiation!0.0085925308502013!5971$GO:0002366!leukocyte activation during immune response!0.0085925308502013!5971$GO:0002285!lymphocyte activation during immune response!0.0085925308502013!5971$GO:0051220!cytoplasmic sequestering of protein!0.0085925308502013!4794$GO:0002293!alpha-beta T cell differentiation during immune response!0.0085925308502013!5971$GO:0002286!T cell activation during immune response!0.0085925308502013!5971$GO:0002263!cell activation during immune response!0.0085925308502013!5971$GO:0042308!negative regulation of protein import into nucleus!0.0085925308502013!4794$GO:0042992!negative regulation of transcription factor import into nucleus!0.0085925308502013!4794$GO:0043367!CD4-positive, alpha beta T cell differentiation!0.0085925308502013!5971$GO:0042088!T-helper 1 type immune response!0.0085925308502013!5971$GO:0046823!negative regulation of nucleocytoplasmic transport!0.0085925308502013!4794$GO:0051224!negative regulation of protein transport!0.00881839046160363!4794$GO:0046632!alpha-beta T cell differentiation!0.0103098228262197!5971$GO:0004709!MAP kinase kinase kinase activity!0.0109026941205202!1326$GO:0046631!alpha-beta T cell activation!0.0109026941205202!5971$GO:0042990!regulation of transcription factor import into nucleus!0.0109026941205202!4794$GO:0042991!transcription factor import into nucleus!0.0109026941205202!4794$GO:0042306!regulation of protein import into nucleus!0.0109026941205202!4794$GO:0033157!regulation of intracellular protein transport!0.0109026941205202!4794$GO:0032507!maintenance of cellular protein localization!0.0111067793515641!4794$GO:0051651!maintenance of cellular localization!0.0111067793515641!4794$GO:0032386!regulation of intracellular transport!0.0111067793515641!4794$GO:0045185!maintenance of protein localization!0.0111656867381263!4794$GO:0002274!myeloid leukocyte activation!0.0112207691804314!5971$GO:0051223!regulation of protein transport!0.0112723852677017!4794$GO:0046822!regulation of nucleocytoplasmic transport!0.0113208501237992!4794$GO:0002573!myeloid leukocyte differentiation!0.0113664417991907!5971$GO:0051051!negative regulation of transport!0.0114094065671464!4794$GO:0030217!T cell differentiation!0.0142699894330178!5971$GO:0051235!maintenance of localization!0.0142699894330178!4794$GO:0030098!lymphocyte differentiation!0.0216742314407406!5971$GO:0002250!adaptive immune response!0.0235842708301034!5971$GO:0002460!adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains!0.0235842708301034!5971$GO:0030099!myeloid cell differentiation!0.0235842708301034!5971$GO:0004702!receptor signaling protein serine/threonine kinase activity!0.0235842708301034!1326$GO:0002521!leukocyte differentiation!0.0269146502620051!5971$GO:0006606!protein import into nucleus!0.0273892766352992!4794$GO:0051170!nuclear import!0.0273892766352992!4794$GO:0042110!T cell activation!0.0273892766352992!5971$GO:0003714!transcription corepressor activity!0.0292605890034004!5971$GO:0051049!regulation of transport!0.0294516884986195!4794$GO:0017038!protein import!0.0319866615733457!4794$GO:0006913!nucleocytoplasmic transport!0.0385026978699054!4794$GO:0046649!lymphocyte activation!0.0385026978699054!5971$GO:0051169!nuclear transport!0.0385026978699054!4794$GO:0030097!hemopoiesis!0.0389812617561175!5971$GO:0048534!hemopoietic or lymphoid organ development!0.0409480756328063!5971$GO:0005057!receptor signaling protein activity!0.0409480756328063!1326$GO:0045321!leukocyte activation!0.0409480756328063!5971$GO:0002520!immune system development!0.0409480756328063!5971$GO:0001775!cell activation!0.0461752674458715!5971$GO:0016564!transcription repressor activity!0.0464717294069291!5971$GO:0006605!protein targeting!0.0465458612671562!4794|id=C2054|ontology_enrichment_celltype=CL:0000738!3.58e-52!136;CL:0000988!2.36e-45!177;CL:0000037!8.71e-45!168;CL:0000566!8.71e-45!168;CL:0002087!1.39e-42!115;CL:0002032!2.79e-42!161;CL:0000837!2.79e-42!161;CL:0002031!3.72e-40!120;CL:0000766!1.34e-32!72;CL:0000557!3.44e-29!67;CL:0002009!2.19e-28!61;CL:0000473!2.30e-27!48;CL:0000234!2.30e-27!48;CL:0002194!4.37e-27!59;CL:0000576!4.37e-27!59;CL:0000040!4.37e-27!59;CL:0000559!4.37e-27!59;CL:0000763!9.49e-27!108;CL:0000049!9.49e-27!108;CL:0000839!3.83e-25!66;CL:0000860!5.13e-25!42;CL:0002057!5.13e-25!42;CL:0000542!7.28e-14!53;CL:0000051!7.28e-14!53;CL:0000838!1.99e-13!52;CL:0002242!2.67e-12!55;CL:0000325!7.30e-11!87;CL:0000134!8.90e-11!354;CL:0002320!1.62e-10!361;CL:0000945!3.14e-10!24;CL:0000826!3.14e-10!24;CL:0000451!2.18e-07!10;CL:0000034!4.91e-07!441|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002193!1.13e-34!108;UBERON:0002390!1.16e-33!98;UBERON:0003061!1.16e-33!98;UBERON:0002405!2.55e-28!93;UBERON:0002371!2.58e-25!76;UBERON:0001474!1.12e-22!82;UBERON:0004765!3.53e-20!90;UBERON:0001434!2.78e-16!100;UBERON:0003081!1.31e-15!203;UBERON:0002384!9.21e-10!371;UBERON:0000178!4.04e-07!15;UBERON:0000179!4.04e-07!15;UBERON:0000463!4.04e-07!15|pathway_enrichment=0.000261809543829384;0.0331450882488;2;268;MAPK signaling pathway (KEGG):04010!4.24401547463794e-05;0.00895487265148605;2;108;T cell receptor signaling pathway (KEGG):04660!2.8113975272981e-07;0.00017796146347797;3;188;TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231!6.25100917324437e-05;0.00989222201665921;2;131;IL-5 up reg. targets (Netpath):NetPath_17!3.88503833680646e-06;0.00122961463359924;2;33;{NFKB1,33} (Static 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|full_id=C2054_Eosinophils_Dendritic_Neutrophils_CD19_CD14_Basophils_CD34
|id=C2054
}}

Latest revision as of 11:57, 17 September 2013


Full id: C2054_Eosinophils_Dendritic_Neutrophils_CD19_CD14_Basophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:30723045..30723060,+p2@MAP3K8
Hg19::chr15:75495066..75495090,-p@chr15:75495066..75495090
-
Hg19::chr19:45504688..45504782,+p1@RELB
Hg19::chr6:44233297..44233330,-p2@NFKBIE


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

p.valueFDRnGenesnPathwayName
0.0002618095438293840.03314508824882268MAPK signaling pathway (KEGG):04010
4.24401547463794e-050.008954872651486052108T cell receptor signaling pathway (KEGG):04660
2.8113975272981e-070.000177961463477973188TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
6.25100917324437e-050.009892222016659212131IL-5 up reg. targets (Netpath):NetPath_17
3.88503833680646e-060.00122961463359924233{NFKB1,33} (Static Module):NA



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:0043011myeloid dendritic cell differentiation0.0085925308502013
GO:0001773myeloid dendritic cell activation0.0085925308502013
GO:0045063T-helper 1 cell differentiation0.0085925308502013
GO:0042994cytoplasmic sequestering of transcription factor0.0085925308502013
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0085925308502013
GO:0002292T cell differentiation during immune response0.0085925308502013
GO:0042093T-helper cell differentiation0.0085925308502013
GO:0002366leukocyte activation during immune response0.0085925308502013
GO:0002285lymphocyte activation during immune response0.0085925308502013
GO:0051220cytoplasmic sequestering of protein0.0085925308502013
GO:0002293alpha-beta T cell differentiation during immune response0.0085925308502013
GO:0002286T cell activation during immune response0.0085925308502013
GO:0002263cell activation during immune response0.0085925308502013
GO:0042308negative regulation of protein import into nucleus0.0085925308502013
GO:0042992negative regulation of transcription factor import into nucleus0.0085925308502013
GO:0043367CD4-positive, alpha beta T cell differentiation0.0085925308502013
GO:0042088T-helper 1 type immune response0.0085925308502013
GO:0046823negative regulation of nucleocytoplasmic transport0.0085925308502013
GO:0051224negative regulation of protein transport0.00881839046160363
GO:0046632alpha-beta T cell differentiation0.0103098228262197
GO:0004709MAP kinase kinase kinase activity0.0109026941205202
GO:0046631alpha-beta T cell activation0.0109026941205202
GO:0042990regulation of transcription factor import into nucleus0.0109026941205202
GO:0042991transcription factor import into nucleus0.0109026941205202
GO:0042306regulation of protein import into nucleus0.0109026941205202
GO:0033157regulation of intracellular protein transport0.0109026941205202
GO:0032507maintenance of cellular protein localization0.0111067793515641
GO:0051651maintenance of cellular localization0.0111067793515641
GO:0032386regulation of intracellular transport0.0111067793515641
GO:0045185maintenance of protein localization0.0111656867381263
GO:0002274myeloid leukocyte activation0.0112207691804314
GO:0051223regulation of protein transport0.0112723852677017
GO:0046822regulation of nucleocytoplasmic transport0.0113208501237992
GO:0002573myeloid leukocyte differentiation0.0113664417991907
GO:0051051negative regulation of transport0.0114094065671464
GO:0030217T cell differentiation0.0142699894330178
GO:0051235maintenance of localization0.0142699894330178
GO:0030098lymphocyte differentiation0.0216742314407406
GO:0002250adaptive immune response0.0235842708301034
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0235842708301034
GO:0030099myeloid cell differentiation0.0235842708301034
GO:0004702receptor signaling protein serine/threonine kinase activity0.0235842708301034
GO:0002521leukocyte differentiation0.0269146502620051
GO:0006606protein import into nucleus0.0273892766352992
GO:0051170nuclear import0.0273892766352992
GO:0042110T cell activation0.0273892766352992
GO:0003714transcription corepressor activity0.0292605890034004
GO:0051049regulation of transport0.0294516884986195
GO:0017038protein import0.0319866615733457
GO:0006913nucleocytoplasmic transport0.0385026978699054
GO:0046649lymphocyte activation0.0385026978699054
GO:0051169nuclear transport0.0385026978699054
GO:0030097hemopoiesis0.0389812617561175
GO:0048534hemopoietic or lymphoid organ development0.0409480756328063
GO:0005057receptor signaling protein activity0.0409480756328063
GO:0045321leukocyte activation0.0409480756328063
GO:0002520immune system development0.0409480756328063
GO:0001775cell activation0.0461752674458715
GO:0016564transcription repressor activity0.0464717294069291
GO:0006605protein targeting0.0465458612671562



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
leukocyte3.58e-52136
hematopoietic cell2.36e-45177
hematopoietic stem cell8.71e-45168
angioblastic mesenchymal cell8.71e-45168
nongranular leukocyte1.39e-42115
hematopoietic oligopotent progenitor cell2.79e-42161
hematopoietic multipotent progenitor cell2.79e-42161
hematopoietic lineage restricted progenitor cell3.72e-40120
myeloid leukocyte1.34e-3272
granulocyte monocyte progenitor cell3.44e-2967
macrophage dendritic cell progenitor2.19e-2861
defensive cell2.30e-2748
phagocyte2.30e-2748
monopoietic cell4.37e-2759
monocyte4.37e-2759
monoblast4.37e-2759
promonocyte4.37e-2759
myeloid cell9.49e-27108
common myeloid progenitor9.49e-27108
myeloid lineage restricted progenitor cell3.83e-2566
classical monocyte5.13e-2542
CD14-positive, CD16-negative classical monocyte5.13e-2542
lymphocyte7.28e-1453
common lymphoid progenitor7.28e-1453
lymphoid lineage restricted progenitor cell1.99e-1352
nucleate cell2.67e-1255
stuff accumulating cell7.30e-1187
mesenchymal cell8.90e-11354
connective tissue cell1.62e-10361
lymphocyte of B lineage3.14e-1024
pro-B cell3.14e-1024
dendritic cell2.18e-0710
stem cell4.91e-07441
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.13e-34108
hematopoietic system1.16e-3398
blood island1.16e-3398
immune system2.55e-2893
bone marrow2.58e-2576
bone element1.12e-2282
skeletal element3.53e-2090
skeletal system2.78e-16100
lateral plate mesoderm1.31e-15203
connective tissue9.21e-10371
blood4.04e-0715
haemolymphatic fluid4.04e-0715
organism substance4.04e-0715


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)
MA0003.13.49532
MA0004.11.69588
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.13.76953
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.11.47358
MA0059.10.604454
MA0060.10.393285
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.15.01475
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.14.54044
MA0103.10.521546
MA0105.12.66951
MA0106.10.869173
MA0107.14.0488
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.11.75643
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.97967
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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
CCNT2#90546.336201576962630.0006203100587215640.00511080484559967
NFKB1#479045.488063424193840.001102199566301980.00766293572793318
PAX5#507946.669565531177830.0005052774169483260.0044292989884729
SIN3A#2594245.408884726815140.001168172384885160.0079392695845006
TAF1#687243.343046285745290.008005664898701650.0321072015804117
ZBTB7A#5134135.513931980906920.009038352821081090.0342174404712686



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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