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Coexpression cluster:C1444: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.515118,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.108006,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;1.2326,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;1.62836,MA0101.1;0.397846,MA0103.1;0.993014,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;1.12205,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;1.61362,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;0.718193,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;1.86512,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;3.64053,MA0065.2;0.718489,MA0150.1;2.10974,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.318517,MA0156.1;1.07131,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.347838,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;1.80563,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;1.43672,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:56, 22 January 2013


Full id: C1444_immature_migratory_CD14_amniotic_Eosinophils_CD19_Neutrophils



Phase1 CAGE Peaks

Hg19::chr18:56338727..56338743,+p3@MALT1
Hg19::chr1:11863148..11863162,-p15@MTHFR
Hg19::chr1:11863171..11863195,-p7@MTHFR
Hg19::chr2:65593835..65593877,-p4@SPRED2
Hg19::chr4:100737954..100738014,+p1@DAPP1
Hg19::chr4:100738030..100738037,+p3@DAPP1


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
4.07274183298443e-050.0257804558027915275B cell receptor signaling pathway (KEGG):04662



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:0019207kinase regulator activity0.00913554713606416
GO:0045859regulation of protein kinase activity0.00913554713606416
GO:0043549regulation of kinase activity0.00913554713606416
GO:0051338regulation of transferase activity0.00913554713606416
GO:0004489methylenetetrahydrofolate reductase (NADPH) activity0.00913554713606416
GO:0032449CBM complex0.00913554713606416
GO:0002711positive regulation of T cell mediated immunity0.00913554713606416
GO:0032743positive regulation of interleukin-2 production0.00913554713606416
GO:0002726positive regulation of T cell cytokine production0.00913554713606416
GO:0002369T cell cytokine production0.00913554713606416
GO:0002724regulation of T cell cytokine production0.00913554713606416
GO:0002702positive regulation of production of molecular mediator of immune response0.00913554713606416
GO:0002720positive regulation of cytokine production during immune response0.00913554713606416
GO:0005173stem cell factor receptor binding0.00913554713606416
GO:0002709regulation of T cell mediated immunity0.00913554713606416
GO:0032663regulation of interleukin-2 production0.00913554713606416
GO:0007243protein kinase cascade0.00913554713606416
GO:0002824positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.00937218767921216
GO:0002718regulation of cytokine production during immune response0.00937218767921216
GO:0002821positive regulation of adaptive immune response0.00937218767921216
GO:0002700regulation of production of molecular mediator of immune response0.00937218767921216
GO:0002367cytokine production during immune response0.00937218767921216
GO:0035014phosphoinositide 3-kinase regulator activity0.00937218767921216
GO:0043621protein self-association0.00937218767921216
GO:0002705positive regulation of leukocyte mediated immunity0.00937218767921216
GO:0002456T cell mediated immunity0.00937218767921216
GO:0002708positive regulation of lymphocyte mediated immunity0.00937218767921216
GO:0002699positive regulation of immune effector process0.00967412384808736
GO:0007250activation of NF-kappaB-inducing kinase0.00967412384808736
GO:0002703regulation of leukocyte mediated immunity0.00967412384808736
GO:0002706regulation of lymphocyte mediated immunity0.00967412384808736
GO:0009086methionine biosynthetic process0.00967412384808736
GO:0002819regulation of adaptive immune response0.00967412384808736
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.00967412384808736
GO:0002697regulation of immune effector process0.0108425657983243
GO:0050790regulation of catalytic activity0.0110794343074728
GO:0009067aspartate family amino acid biosynthetic process0.0111055472779436
GO:0050852T cell receptor signaling pathway0.0111055472779436
GO:0006555methionine metabolic process0.0111055472779436
GO:0019209kinase activator activity0.0111055472779436
GO:0000188inactivation of MAPK activity0.0111055472779436
GO:0065009regulation of a molecular function0.0114971521612877
GO:0005942phosphoinositide 3-kinase complex0.0114971521612877
GO:0000097sulfur amino acid biosynthetic process0.0114971521612877
GO:0032623interleukin-2 production0.0118032216391385
GO:0001819positive regulation of cytokine production0.0126451920081803
GO:0043407negative regulation of MAP kinase activity0.0129136683529758
GO:0002440production of molecular mediator of immune response0.0138461843222623
GO:0050851antigen receptor-mediated signaling pathway0.0138461843222623
GO:0009966regulation of signal transduction0.0138461843222623
GO:0009066aspartate family amino acid metabolic process0.0138818511611803
GO:0000096sulfur amino acid metabolic process0.0141005159226811
GO:0002429immune response-activating cell surface receptor signaling pathway0.0143108870724969
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0145134253692679
GO:0002757immune response-activating signal transduction0.0147085580619147
GO:0002764immune response-regulating signal transduction0.014896681881578
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.0150781657186168
GO:0050870positive regulation of T cell activation0.0175607085218321
GO:0001817regulation of cytokine production0.0175607085218321
GO:0005515protein binding0.0176817365756131
GO:0051168nuclear export0.0180470171372814
GO:0032501multicellular organismal process0.0180470171372814
GO:0044272sulfur compound biosynthetic process0.0180470171372814
GO:0030693caspase activity0.0197345665058968
GO:0051251positive regulation of lymphocyte activation0.0198187015967892
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.019900253366686
GO:0006469negative regulation of protein kinase activity0.0211674835851774
GO:0033673negative regulation of kinase activity0.0211674835851774
GO:0051348negative regulation of transferase activity0.021282316428579
GO:0050863regulation of T cell activation0.021282316428579
GO:0051259protein oligomerization0.0220465540844657
GO:0032147activation of protein kinase activity0.0245368867182962
GO:0002253activation of immune response0.0245454059728686
GO:0002449lymphocyte mediated immunity0.0245536648911535
GO:0002250adaptive immune response0.0249035740846093
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0249035740846093
GO:0051249regulation of lymphocyte activation0.0249035740846093
GO:0002443leukocyte mediated immunity0.0252290237302291
GO:0050865regulation of cell activation0.0255461214629594
GO:0008652amino acid biosynthetic process0.0261196739881982
GO:0050778positive regulation of immune response0.0261196739881982
GO:0006790sulfur metabolic process0.0261196739881982
GO:0002684positive regulation of immune system process0.0261196739881982
GO:0043086negative regulation of catalytic activity0.0261196739881982
GO:0043405regulation of MAP kinase activity0.027585235601085
GO:0050776regulation of immune response0.0283196817116856
GO:0042110T cell activation0.0283196817116856
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0283196817116856
GO:0002682regulation of immune system process0.0283196817116856
GO:0007165signal transduction0.0290757114283303
GO:0051240positive regulation of multicellular organismal process0.0290757114283303
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0295774556148059
GO:0002252immune effector process0.0297986264495236
GO:0001816cytokine production0.0302816501657053
GO:0009309amine biosynthetic process0.0315454828143631
GO:0007154cell communication0.0344384781344397
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0360556320903252
GO:0045860positive regulation of protein kinase activity0.0360849101192422
GO:0004197cysteine-type endopeptidase activity0.0360849101192422
GO:0033674positive regulation of kinase activity0.0362240154231583
GO:0044271nitrogen compound biosynthetic process0.0362488046806512
GO:0051347positive regulation of transferase activity0.0362488046806512
GO:0000165MAPKKK cascade0.0365640539599067
GO:0009967positive regulation of signal transduction0.0365640539599067
GO:0006913nucleocytoplasmic transport0.0365640539599067
GO:0046649lymphocyte activation0.0365640539599067
GO:0051169nuclear transport0.0365640539599067
GO:0007242intracellular signaling cascade0.0365640539599067
GO:0008015blood circulation0.0365640539599067
GO:0003013circulatory system process0.0365640539599067
GO:0004842ubiquitin-protein ligase activity0.0371339497738497
GO:0008639small protein conjugating enzyme activity0.037247914142536
GO:0006916anti-apoptosis0.0378012012049799
GO:0045321leukocyte activation0.0396561771719475
GO:0044445cytosolic part0.0414769691378795
GO:0043687post-translational protein modification0.0440000489858293
GO:0001775cell activation0.0448071134385577
GO:0004725protein tyrosine phosphatase activity0.0463221020896512
GO:0043066negative regulation of apoptosis0.0478101264284914
GO:0043069negative regulation of programmed cell death0.0480319249969728
GO:0019787small conjugating protein ligase activity0.049888895594376



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
leukocyte5.61e-33136
nongranular leukocyte1.11e-31115
hematopoietic lineage restricted progenitor cell4.58e-29120
classical monocyte4.36e-2642
CD14-positive, CD16-negative classical monocyte4.36e-2642
macrophage dendritic cell progenitor3.48e-2561
hematopoietic stem cell3.26e-24168
angioblastic mesenchymal cell3.26e-24168
hematopoietic cell4.09e-24177
monopoietic cell1.01e-2359
monocyte1.01e-2359
monoblast1.01e-2359
promonocyte1.01e-2359
defensive cell1.40e-2348
phagocyte1.40e-2348
granulocyte monocyte progenitor cell6.34e-2367
hematopoietic oligopotent progenitor cell4.17e-22161
hematopoietic multipotent progenitor cell4.17e-22161
myeloid lineage restricted progenitor cell5.16e-2166
myeloid leukocyte6.29e-2072
myeloid cell7.80e-14108
common myeloid progenitor7.80e-14108
lymphocyte of B lineage2.43e-1124
pro-B cell2.43e-1124
lymphocyte3.00e-0853
common lymphoid progenitor3.00e-0853
lymphoid lineage restricted progenitor cell7.98e-0852
nucleate cell1.02e-0755
B cell1.51e-0714
dendritic cell1.72e-0710
endo-epithelial cell3.76e-0742
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.15e-2298
blood island3.15e-2298
bone marrow2.68e-1876
hemolymphoid system2.41e-17108
bone element3.82e-1582
immune system4.31e-1593
skeletal element6.10e-1590
skeletal system4.37e-13100


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
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
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
MA0048.10.152639
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.2326
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.11.62836
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.21.86512
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.23.64053
MA0065.20.718489
MA0150.12.10974
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.273773
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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
POLR2A#543062.147453176558070.01019570676818780.0380309803622546
SRF#6722511.49764855180651.12681431027194e-050.000288157100270546
TCF12#693835.317232451093210.013367345733860.0472476046127861
TFAP2C#702235.404614304930110.01277576166695870.0460639291837155



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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