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Coexpression cluster:C4399: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,1.44641,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,1.55552,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,3.57034,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,1.44641,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,1.55552,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,3.57034,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;1.62115,MA0050.1;6.01961,MA0051.1;5.06231,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;2.26659,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;1.55947,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;2.91906,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;2.32251,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;2.28794,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 22:02, 22 January 2013


Full id: C4399_Neutrophils_CD14_Whole_Eosinophils_CD19_migratory_spleen



Phase1 CAGE Peaks

Hg19::chr4:185395633..185395651,-p2@IRF2
Hg19::chr6:32806472..32806481,-p7@TAP2
Hg19::chr6:32806483..32806503,-p3@TAP2


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:0004409homoaconitate hydratase activity0.00322604381779525
GO:0046967cytosol to ER transport0.00322604381779525
GO:0042825TAP complex0.00322604381779525
GO:0015433peptide antigen-transporting ATPase activity0.00322604381779525
GO:0015440peptide-transporting ATPase activity0.00322604381779525
GO:0046980tapasin binding0.00322604381779525
GO:0046977TAP binding0.00322604381779525
GO:0042824MHC class I peptide loading complex0.00322604381779525
GO:0046979TAP2 binding0.00322604381779525
GO:0046978TAP1 binding0.00322604381779525
GO:0042301phosphate binding0.00403243606120116
GO:0015198oligopeptide transporter activity0.00403243606120116
GO:0015197peptide transporter activity0.00496285212327168
GO:0042288MHC class I protein binding0.00518433170739016
GO:0002483antigen processing and presentation of endogenous peptide antigen0.00763905561147222
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.00763905561147222
GO:0006857oligopeptide transport0.00763905561147222
GO:0042605peptide antigen binding0.00763905561147222
GO:0019883antigen processing and presentation of endogenous antigen0.00763905561147222
GO:0042287MHC protein binding0.00927228213987372
GO:0015833peptide transport0.0149703443648315
GO:0005788endoplasmic reticulum lumen0.0234414163837479
GO:0016836hydro-lyase activity0.0313176878355985
GO:0016835carbon-oxygen lyase activity0.0313176878355985
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0313176878355985
GO:0048002antigen processing and presentation of peptide antigen0.0313176878355985
GO:0046982protein heterodimerization activity0.0313176878355985
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0365148045338801
GO:0042803protein homodimerization activity0.0438413389976883
GO:0003823antigen binding0.0474629779509783



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
leukocyte9.47e-52136
nongranular leukocyte1.45e-45115
hematopoietic stem cell4.59e-42168
angioblastic mesenchymal cell4.59e-42168
hematopoietic lineage restricted progenitor cell9.30e-42120
hematopoietic cell2.67e-41177
hematopoietic oligopotent progenitor cell1.44e-39161
hematopoietic multipotent progenitor cell1.44e-39161
myeloid leukocyte2.56e-2872
macrophage dendritic cell progenitor7.05e-2661
monopoietic cell9.83e-2659
monocyte9.83e-2659
monoblast9.83e-2659
promonocyte9.83e-2659
granulocyte monocyte progenitor cell2.09e-2467
myeloid lineage restricted progenitor cell2.32e-2366
defensive cell1.01e-2248
phagocyte1.01e-2248
classical monocyte4.38e-2142
CD14-positive, CD16-negative classical monocyte4.38e-2142
myeloid cell6.24e-21108
common myeloid progenitor6.24e-21108
lymphocyte1.18e-1753
common lymphoid progenitor1.18e-1753
nucleate cell2.60e-1755
lymphoid lineage restricted progenitor cell2.68e-1752
mesenchymal cell2.22e-12354
connective tissue cell2.96e-12361
lymphocyte of B lineage2.13e-1124
pro-B cell2.13e-1124
B cell5.14e-0914
motile cell5.99e-08386
multi fate stem cell7.54e-07427
stuff accumulating cell9.76e-0787
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.76e-34108
hematopoietic system6.03e-3398
blood island6.03e-3398
immune system9.36e-2693
bone marrow4.33e-2276
bone element7.23e-1882
skeletal element6.79e-1790
skeletal system1.60e-14100
lateral plate mesoderm2.69e-14203
connective tissue1.82e-11371
blood2.21e-0915
haemolymphatic fluid2.21e-0915
organism substance2.21e-0915


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.16.01961
MA0051.15.06231
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.26659
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.12.91906
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.12.32251
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCLAF1#9774214.43509840674790.006201147435546130.0273960083342217
CCNT2#90536.336201576962630.003930750035764890.0190728304676291
ELF1#199734.258097958807540.01295179875054610.0464166120962282
ETS1#211339.728760922202340.001085840092584840.00764229755572934
FOSL1#8061226.47571981091530.001869833702590980.0110279852080923
HMGN3#932438.178547723350590.001827766942164210.0108999115898298
IRF1#365937.63716375356390.002244692747297240.0128527119427071
MAX#414936.452555509007120.003721913834265510.0187178195664687
MEF2A#4205318.74323090964410.0001518243905622470.00195323817762139
MXI1#460139.96157162875930.001011470541259020.00722106581848048
NFKB1#479035.488063424193840.006049381815655430.0270447064528589
PAX5#507936.669565531177830.003370290999677260.0173445265455452
POU2F2#545239.106124057742520.001324165192682130.00884518634848282
PRDM1#639287.88730385164050.0001716248848029080.00209249723837625
RAD21#5885310.35503389545630.0009004912073565420.00666759313754767
RFX5#5993312.04791082719510.0005717246050312580.00485924039915849
RXRA#6256213.38307809275550.007196434429465730.0298367771091295
SIN3A#2594235.408884726815140.006318961977991520.027777846199994
SMARCB1#6598212.16847718743830.008675002221921740.0330069786533311
SMC3#9126210.02995522995520.0126656379767470.0457759132315978
SPI1#668838.204323508522730.001810593189410520.0109304359600488
STAT1#6772320.70658749719920.0001125992441046670.00155182798298328
STAT2#6773365.26377118644073.59360517547754e-060.000118544703386513
THAP1#55145220.91276306856750.002983447413736940.0158754911317711
YY1#752834.911170749853860.008441455341808260.0330627097109737
ZBTB7A#5134137.35190930787590.002516255860282270.0140675148970622
ZNF263#1012738.221841637010680.001799043925565870.0109806760880237



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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