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Coexpression cluster:C537: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.196975,MA0004.1;0.631966,MA0006.1;0.362024,MA0007.1;0.208008,MA0009.1;0.621697,MA0014.1;0.0424137,MA0017.1;0.425352,MA0019.1;0.340029,MA0024.1;0.525161,MA0025.1;0.747404,MA0027.1;2.20546,MA0028.1;0.122394,MA0029.1;0.542771,MA0030.1;0.532314,MA0031.1;0.474026,MA0038.1;0.302644,MA0040.1;0.548121,MA0041.1;1.2374,MA0042.1;0.608306,MA0043.1;0.621991,MA0046.1;0.611559,MA0048.1;0.0663643,MA0050.1;0.212584,MA0051.1;0.299199,MA0052.1;0.551663,MA0055.1;0.0307766,MA0056.1;0,MA0057.1;0.0128587,MA0058.1;0.467197,MA0059.1;0.15289,MA0060.1;0.18988,MA0061.1;0.0397345,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;0.111262,MA0069.1;0.607975,MA0070.1;0.597583,MA0071.1;0.27142,MA0072.1;0.593415,MA0073.1;0.000143211,MA0074.1;0.298586,MA0076.1;0.164578,MA0077.1;0.586275,MA0078.1;0.995054,MA0081.1;0.465308,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;1.44255,MA0088.1;0.0797435,MA0089.1;0,MA0090.1;0.518617,MA0091.1;0.223914,MA0092.1;1.08245,MA0093.1;0.740148,MA0095.1;0,MA0098.1;0,MA0100.1;0.843378,MA0101.1;0.116395,MA0103.1;0.34743,MA0105.1;0.14145,MA0106.1;0.33677,MA0107.1;0.0748038,MA0108.2;1.18798,MA0109.1;0,MA0111.1;0.184188,MA0113.1;0.924932,MA0114.1;0.072201,MA0115.1;0.850405,MA0116.1;0.0765991,MA0117.1;0.656858,MA0119.1;0.142224,MA0122.1;0.681203,MA0124.1;0.810546,MA0125.1;0.730403,MA0130.1;0,MA0131.1;0.398042,MA0132.1;0,MA0133.1;0,MA0135.1;0.650071,MA0136.1;0.830767,MA0139.1;0.327572,MA0140.1;0.74193,MA0141.1;0.462123,MA0142.1;0.445733,MA0143.1;0.350722,MA0144.1;0.231909,MA0145.1;0.0322091,MA0146.1;0.603856,MA0147.1;0.269778,MA0148.1;0.240905,MA0149.1;0.261654,MA0062.2;0.148712,MA0035.2;0.268747,MA0039.2;0.750837,MA0138.2;0.38342,MA0002.2;0.393994,MA0137.2;0.398112,MA0104.2;0.420925,MA0047.2;0.326636,MA0112.2;0.339585,MA0065.2;0.033787,MA0150.1;0.98029,MA0151.1;0,MA0152.1;1.381,MA0153.1;0.714423,MA0154.1;0.137179,MA0155.1;0.025611,MA0156.1;0.12788,MA0157.1;0.421609,MA0158.1;0,MA0159.1;0.270712,MA0160.1;0.252705,MA0161.1;0,MA0162.1;0.259032,MA0163.1;0.00623,MA0164.1;0.361105,MA0080.2;0.740384,MA0018.2;0.337929,MA0099.2;0.754549,MA0079.2;0.00137008,MA0102.2;1.14323,MA0258.1;0.218609,MA0259.1;0.28219,MA0442.1;0
}}
}}

Revision as of 19:15, 22 January 2013


Full id: C537_immature_CD14_migratory_Mast_CD4_Dendritic_Basophils



Phase1 CAGE Peaks

Hg19::chr12:100967533..100967548,+p3@GAS2L3
Hg19::chr13:99948360..99948387,-p5@GPR183
Hg19::chr13:99959641..99959660,-p1@GPR183
Hg19::chr16:11670817..11670855,-p@chr16:11670817..11670855
-
Hg19::chr18:56338201..56338239,+p8@MALT1
Hg19::chr18:56338750..56338823,+p2@MALT1
Hg19::chr1:192544895..192544912,+p1@RGS1
Hg19::chr1:192545731..192545733,+p@chr1:192545731..192545733
+
Hg19::chr1:192548520..192548535,+p@chr1:192548520..192548535
+
Hg19::chr1:192548540..192548575,+p@chr1:192548540..192548575
+
Hg19::chr1:192578548..192578577,+p@chr1:192578548..192578577
+
Hg19::chr1:206756466..206756481,+p15@RASSF5
Hg19::chr1:206756498..206756508,+p13@RASSF5
Hg19::chr2:201997492..201997510,+p22@CFLAR
Hg19::chr6:134495992..134496010,-p1@SGK1
Hg19::chr7:6066589..6066602,-p4@EIF2AK1
Hg19::chr9:134505871..134505884,-p@chr9:134505871..134505884
-


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:0048523negative regulation of cellular process2.24315862494925e-07
GO:0048519negative regulation of biological process2.24315862494925e-07
GO:0050794regulation of cellular process0.0017810822156576
GO:0030693caspase activity0.0017810822156576
GO:0050789regulation of biological process0.0017810822156576
GO:0065007biological regulation0.00257669638261057
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.00376780878370422
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.00376780878370422
GO:0007242intracellular signaling cascade0.00376780878370422
GO:0046984regulation of hemoglobin biosynthetic process0.00376780878370422
GO:0046986negative regulation of hemoglobin biosynthetic process0.00376780878370422
GO:0045993negative regulation of translational initiation by iron0.00376780878370422
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0042882600480954
GO:0009966regulation of signal transduction0.0042882600480954
GO:0004197cysteine-type endopeptidase activity0.0042882600480954
GO:0009967positive regulation of signal transduction0.0042882600480954
GO:0006915apoptosis0.0042882600480954
GO:0012501programmed cell death0.0042882600480954
GO:0006447regulation of translational initiation by iron0.0042882600480954
GO:0016265death0.0042882600480954
GO:0008219cell death0.0042882600480954
GO:0006916anti-apoptosis0.0042882600480954
GO:0032449CBM complex0.00583273858869478
GO:0045786negative regulation of progression through cell cycle0.00583273858869478
GO:0043066negative regulation of apoptosis0.00583273858869478
GO:0043069negative regulation of programmed cell death0.00583273858869478
GO:0004694eukaryotic translation initiation factor 2alpha kinase activity0.00583273858869478
GO:0042541hemoglobin biosynthetic process0.00583273858869478
GO:0002711positive regulation of T cell mediated immunity0.00583273858869478
GO:0002726positive regulation of T cell cytokine production0.00583273858869478
GO:0032743positive regulation of interleukin-2 production0.00583273858869478
GO:0002369T cell cytokine production0.00656329538340829
GO:0020027hemoglobin metabolic process0.00656329538340829
GO:0002724regulation of T cell cytokine production0.00656329538340829
GO:0048468cell development0.00656329538340829
GO:0002720positive regulation of cytokine production during immune response0.00695339556003099
GO:0002709regulation of T cell mediated immunity0.00695339556003099
GO:0002702positive regulation of production of molecular mediator of immune response0.00695339556003099
GO:0032663regulation of interleukin-2 production0.00695339556003099
GO:0008234cysteine-type peptidase activity0.00724077483814711
GO:0000074regulation of progression through cell cycle0.00859537530791841
GO:0002824positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.00859537530791841
GO:0002718regulation of cytokine production during immune response0.00859537530791841
GO:0002700regulation of production of molecular mediator of immune response0.00859537530791841
GO:0002821positive regulation of adaptive immune response0.00859537530791841
GO:0002367cytokine production during immune response0.00859537530791841
GO:0045947negative regulation of translational initiation0.00859537530791841
GO:0051726regulation of cell cycle0.00859537530791841
GO:0043621protein self-association0.00859537530791841
GO:0002705positive regulation of leukocyte mediated immunity0.00859537530791841
GO:0002456T cell mediated immunity0.00859537530791841
GO:0002708positive regulation of lymphocyte mediated immunity0.00859537530791841
GO:0007243protein kinase cascade0.00859537530791841
GO:0002699positive regulation of immune effector process0.00920342365642115
GO:0007250activation of NF-kappaB-inducing kinase0.0095109723453188
GO:0002703regulation of leukocyte mediated immunity0.0095109723453188
GO:0002706regulation of lymphocyte mediated immunity0.0095109723453188
GO:0002819regulation of adaptive immune response0.00995354786076241
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.00995354786076241
GO:0008047enzyme activator activity0.0108648337132161
GO:0002697regulation of immune effector process0.0108648337132161
GO:0048869cellular developmental process0.0108648337132161
GO:0030154cell differentiation0.0108648337132161
GO:0050852T cell receptor signaling pathway0.0119957574765944
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.012315593328365
GO:0019209kinase activator activity0.012315593328365
GO:0032623interleukin-2 production0.0141506172788111
GO:0042981regulation of apoptosis0.015046854486826
GO:0001819positive regulation of cytokine production0.015046854486826
GO:0043067regulation of programmed cell death0.0150471991741007
GO:0002440production of molecular mediator of immune response0.0169227294353164
GO:0050851antigen receptor-mediated signaling pathway0.0169227294353164
GO:0022402cell cycle process0.0169247527158631
GO:0002429immune response-activating cell surface receptor signaling pathway0.0182908043949664
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0186471190494062
GO:0002757immune response-activating signal transduction0.0189939697488288
GO:0002764immune response-regulating signal transduction0.019331725228904
GO:0008624induction of apoptosis by extracellular signals0.0195617293708246
GO:0007165signal transduction0.0195617293708246
GO:0005515protein binding0.0195617293708246
GO:0065003macromolecular complex assembly0.0220037306241794
GO:0017148negative regulation of translation0.0220037306241794
GO:0050870positive regulation of T cell activation0.0220037306241794
GO:0001817regulation of cytokine production0.0220037306241794
GO:0046777protein amino acid autophosphorylation0.0228721929696117
GO:0051168nuclear export0.0228721929696117
GO:0004175endopeptidase activity0.0228721929696117
GO:0031327negative regulation of cellular biosynthetic process0.0228721929696117
GO:0022607cellular component assembly0.0228721929696117
GO:0016540protein autoprocessing0.0228721929696117
GO:0007154cell communication0.0228721929696117
GO:0007049cell cycle0.0238033305506717
GO:0051251positive regulation of lymphocyte activation0.0244407496816509
GO:0009890negative regulation of biosynthetic process0.0244407496816509
GO:0006446regulation of translational initiation0.0265446408743006
GO:0019992diacylglycerol binding0.0273839977685522
GO:0050863regulation of T cell activation0.0273839977685522
GO:0051259protein oligomerization0.0283440663215144
GO:0048522positive regulation of cellular process0.0283440663215144
GO:0032147activation of protein kinase activity0.031489309870482
GO:0002253activation of immune response0.0316206014706882
GO:0002449lymphocyte mediated immunity0.0317492540192714
GO:0002250adaptive immune response0.0325284149901371
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0325284149901371
GO:0051249regulation of lymphocyte activation0.0325284149901371
GO:0048518positive regulation of biological process0.0325284149901371
GO:0002443leukocyte mediated immunity0.0327733114089864
GO:0050865regulation of cell activation0.0332975156710067
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0345909721499402
GO:0050778positive regulation of immune response0.0345909721499402
GO:0002684positive regulation of immune system process0.0345909721499402
GO:0032502developmental process0.0345909721499402
GO:0019933cAMP-mediated signaling0.0345909721499402
GO:0006955immune response0.0375347261122997
GO:0042110T cell activation0.0376609939647763
GO:0050776regulation of immune response0.0376609939647763
GO:0006413translational initiation0.0376609939647763
GO:0016485protein processing0.0376609939647763
GO:0002682regulation of immune system process0.0377189576754196
GO:0007050cell cycle arrest0.0377759005116457
GO:0008233peptidase activity0.0379408528307297
GO:0051248negative regulation of protein metabolic process0.0379408528307297
GO:0009968negative regulation of signal transduction0.0379408528307297
GO:0051240positive regulation of multicellular organismal process0.0379939572091468
GO:0002252immune effector process0.0394702486707968
GO:0001816cytokine production0.0402160355131639
GO:0004871signal transducer activity0.0402866767778344
GO:0060089molecular transducer activity0.0402866767778344
GO:0006508proteolysis0.0402866767778344
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0403465209399871
GO:0019935cyclic-nucleotide-mediated signaling0.0414180612908684
GO:0019207kinase regulator activity0.0414180612908684
GO:0002376immune system process0.0430407520909788
GO:0022618protein-RNA complex assembly0.046395642167172
GO:0045860positive regulation of protein kinase activity0.046395642167172
GO:0005516calmodulin binding0.046395642167172
GO:0033674positive regulation of kinase activity0.0470265471912302
GO:0051347positive regulation of transferase activity0.0476478819210036
GO:0006913nucleocytoplasmic transport0.0494565020587583
GO:0046649lymphocyte activation0.0494565020587583
GO:0051169nuclear transport0.0494565020587583
GO:0042803protein homodimerization activity0.0497304947002505



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
myeloid leukocyte4.13e-8972
leukocyte1.73e-87136
granulocyte monocyte progenitor cell7.30e-8767
macrophage dendritic cell progenitor4.73e-8661
classical monocyte2.23e-8342
CD14-positive, CD16-negative classical monocyte2.23e-8342
defensive cell2.19e-8248
phagocyte2.19e-8248
monopoietic cell1.18e-8159
monocyte1.18e-8159
monoblast1.18e-8159
promonocyte1.18e-8159
myeloid lineage restricted progenitor cell5.08e-8166
hematopoietic lineage restricted progenitor cell2.58e-68120
nongranular leukocyte7.98e-67115
hematopoietic stem cell9.45e-67168
angioblastic mesenchymal cell9.45e-67168
myeloid cell2.05e-65108
common myeloid progenitor2.05e-65108
hematopoietic cell2.91e-62177
hematopoietic oligopotent progenitor cell1.30e-60161
hematopoietic multipotent progenitor cell1.30e-60161
stuff accumulating cell6.11e-3987
dendritic cell1.95e-2010
mesenchymal cell2.27e-20354
connective tissue cell1.46e-19361
intermediate monocyte2.17e-179
CD14-positive, CD16-positive monocyte2.17e-179
conventional dendritic cell3.64e-178
motile cell9.91e-17386
multi fate stem cell2.70e-13427
stem cell7.35e-13441
somatic stem cell8.00e-13433
immature conventional dendritic cell3.92e-125
common dendritic progenitor3.92e-125
Langerhans cell6.28e-115
basophil5.62e-073
single nucleate cell9.50e-073
mononuclear cell9.50e-073
Uber Anatomy
Ontology termp-valuen
bone marrow1.14e-7476
hematopoietic system2.07e-7298
blood island2.07e-7298
immune system1.34e-7193
bone element5.17e-6882
hemolymphoid system3.98e-66108
skeletal element1.64e-6090
skeletal system8.18e-53100
musculoskeletal system3.56e-26167
lateral plate mesoderm1.29e-25203
connective tissue3.23e-19371
mesoderm1.25e-11315
mesoderm-derived structure1.25e-11315
presumptive mesoderm1.25e-11315


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)
MA0003.10.196975
MA0004.10.631966
MA0006.10.362024
MA0007.10.208008
MA0009.10.621697
MA0014.10.0424137
MA0017.10.425352
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.11.2374
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.0663643
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.0307766
MA0056.10
MA0057.10.0128587
MA0058.10.467197
MA0059.10.15289
MA0060.10.18988
MA0061.10.0397345
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.000143211
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.995054
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.11.44255
MA0088.10.0797435
MA0089.10
MA0090.10.518617
MA0091.10.223914
MA0092.11.08245
MA0093.10.740148
MA0095.10
MA0098.10
MA0100.10.843378
MA0101.10.116395
MA0103.10.34743
MA0105.10.14145
MA0106.10.33677
MA0107.10.0748038
MA0108.21.18798
MA0109.10
MA0111.10.184188
MA0113.10.924932
MA0114.10.072201
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.830767
MA0139.10.327572
MA0140.10.74193
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.231909
MA0145.10.0322091
MA0146.10.603856
MA0147.10.269778
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.268747
MA0039.20.750837
MA0138.20.38342
MA0002.20.393994
MA0137.20.398112
MA0104.20.420925
MA0047.20.326636
MA0112.20.339585
MA0065.20.033787
MA0150.10.98029
MA0151.10
MA0152.11.381
MA0153.10.714423
MA0154.10.137179
MA0155.10.025611
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.10.259032
MA0163.10.00623
MA0164.10.361105
MA0080.20.740384
MA0018.20.337929
MA0099.20.754549
MA0079.20.00137008
MA0102.21.14323
MA0258.10.218609
MA0259.10.28219
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
BATF#1053845.731247480542030.004394533429899440.020823987154504
BCL11A#5333558.343957383413840.0002355864089118190.00256723799669673
EBF1#187994.715188330536532.94711196653903e-050.000614235535169367
GATA3#262546.408592084048470.002942384100404120.0156993794350723
MEF2A#420555.512714973424720.001555360612452480.00987839376088085
MEF2C#420849.720318704146840.0006338379637329130.00520174470330832
NFKB1#4790134.196754383207052.76672721519416e-071.40405356476027e-05
POU2F2#545294.820889207040162.46150792069039e-050.000533577056307562
SMC3#912654.424980248509660.004076926588776390.0194780483076494
SPI1#668883.860858121657750.0004245192060962430.00396781469173845
SRF#672264.869592327823930.0008899599272497780.00662956667917543
USF2#739275.349728335028650.0001554195827960840.00198070357628313



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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