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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:25, 17 September 2013


Full id: C532_Mast_CD14_Eosinophils_seminal_ductus_Neutrophils_Smooth



Phase1 CAGE Peaks

Hg19::chr11:5705095..5705101,+p@chr11:5705095..5705101
+
Hg19::chr17:32580142..32580147,+p@chr17:32580142..32580147
+
Hg19::chr17:7747016..7747035,+p@chr17:7747016..7747035
+
Hg19::chr17:7748946..7748974,+p1@AB383855
Hg19::chr17:7749478..7749496,+p@chr17:7749478..7749496
+
Hg19::chr17:7750261..7750276,+p@chr17:7750261..7750276
+
Hg19::chr17:7750417..7750437,+p10@KDM6B
Hg19::chr1:186649543..186649563,-p1@PTGS2
Hg19::chr1:31205338..31205351,-p5@LAPTM5
Hg19::chr2:9695787..9695813,-p3@ADAM17
Hg19::chr2:9695820..9695831,-p5@ADAM17
Hg19::chr3:10291107..10291123,-p1@BC009749
Hg19::chr5:148206163..148206201,+p1@ADRB2
Hg19::chr5:75839007..75839024,+p@chr5:75839007..75839024
+
Hg19::chr6:144127704..144127730,+p1@ENST00000545614
Hg19::chr6:2889928..2889934,-p@chr6:2889928..2889934
-
Hg19::chrX:110924878..110924902,+p3@ALG13


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:0031347regulation of defense response0.000978689551586044
GO:0050727regulation of inflammatory response0.000978689551586044
GO:0048583regulation of response to stimulus0.00108557781968457
GO:0048589developmental growth0.00108557781968457
GO:0008217regulation of blood pressure0.00193438366969393
GO:0044459plasma membrane part0.00308260397451496
GO:0048636positive regulation of muscle development0.00308260397451496
GO:0048631regulation of skeletal muscle growth0.00308260397451496
GO:0004941beta2-adrenergic receptor activity0.00308260397451496
GO:0002032arrestin mediated desensitization of G-protein coupled receptor protein signaling pathway0.00308260397451496
GO:0004577N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity0.00308260397451496
GO:0048638regulation of developmental growth0.00308260397451496
GO:0019371cyclooxygenase pathway0.00308260397451496
GO:0051927negative regulation of calcium ion transport via voltage-gated calcium channel0.00308260397451496
GO:0048630skeletal muscle growth0.00308260397451496
GO:0048639positive regulation of developmental growth0.00308260397451496
GO:0048643positive regulation of skeletal muscle development0.00308260397451496
GO:0048633positive regulation of skeletal muscle growth0.00308260397451496
GO:0008015blood circulation0.00382645550491927
GO:0003013circulatory system process0.00382645550491927
GO:0002021response to dietary excess0.00382645550491927
GO:0048641regulation of skeletal muscle development0.00382645550491927
GO:0051930regulation of sensory perception of pain0.00382645550491927
GO:0051380norepinephrine binding0.00382645550491927
GO:0044246regulation of multicellular organismal metabolic process0.00382645550491927
GO:0002025norepinephrine-epinephrine vasodilation involved in regulation of systemic arterial blood pressure0.00382645550491927
GO:0044253positive regulation of multicellular organismal metabolic process0.00382645550491927
GO:0002024diet induced thermogenesis0.00382645550491927
GO:0051931regulation of sensory perception0.00382645550491927
GO:0005764lysosome0.0040595369483209
GO:0000323lytic vacuole0.0040595369483209
GO:0007171transmembrane receptor protein tyrosine kinase activation (dimerization)0.0040595369483209
GO:0004666prostaglandin-endoperoxide synthase activity0.0040595369483209
GO:0051926negative regulation of calcium ion transport0.0040595369483209
GO:0022401adaptation of signaling pathway0.0040595369483209
GO:0051925regulation of calcium ion transport via voltage-gated calcium channel0.0040595369483209
GO:0002029desensitization of G-protein coupled receptor protein signaling pathway0.0040595369483209
GO:0045932negative regulation of muscle contraction0.0040595369483209
GO:0048634regulation of muscle development0.0040595369483209
GO:0045986negative regulation of smooth muscle contraction0.0040595369483209
GO:0030501positive regulation of bone mineralization0.0040595369483209
GO:0005773vacuole0.00414753281572236
GO:0005737cytoplasm0.0041869488270513
GO:0005887integral to plasma membrane0.0041869488270513
GO:0031226intrinsic to plasma membrane0.0041869488270513
GO:0002028regulation of sodium ion transport0.0041869488270513
GO:0031649heat generation0.0041869488270513
GO:0045744negative regulation of G-protein coupled receptor protein signaling pathway0.0041869488270513
GO:0043271negative regulation of ion transport0.0041869488270513
GO:0040015negative regulation of multicellular organism growth0.0041869488270513
GO:0045909positive regulation of vasodilation0.0041869488270513
GO:0019369arachidonic acid metabolic process0.0041869488270513
GO:0004939beta-adrenergic receptor activity0.0041869488270513
GO:0006954inflammatory response0.00454703326356174
GO:0005886plasma membrane0.00454703326356174
GO:0042640anagen0.00454703326356174
GO:0003085negative regulation of systemic arterial blood pressure0.00454703326356174
GO:0030259lipid glycosylation0.00454703326356174
GO:0045823positive regulation of heart contraction0.00454703326356174
GO:0001993regulation of systemic arterial blood pressure by norepinephrine-epinephrine0.00454703326356174
GO:0050873brown fat cell differentiation0.00454703326356174
GO:0009888tissue development0.00479875604839804
GO:0008333endosome to lysosome transport0.0051203575259798
GO:0042312regulation of vasodilation0.0051203575259798
GO:0045778positive regulation of ossification0.0051203575259798
GO:0048820hair follicle maturation0.00570986645212989
GO:0046852positive regulation of bone remodeling0.00570986645212989
GO:0001659thermoregulation0.00570986645212989
GO:0009409response to cold0.00616266761559062
GO:0045776negative regulation of blood pressure0.00616266761559062
GO:0043410positive regulation of MAPKKK cascade0.00616266761559062
GO:0030279negative regulation of ossification0.00616266761559062
GO:0031348negative regulation of defense response0.00674522552025061
GO:0050728negative regulation of inflammatory response0.00674522552025061
GO:0001516prostaglandin biosynthetic process0.00728100014777047
GO:0046457prostanoid biosynthetic process0.00728100014777047
GO:0044444cytoplasmic part0.00728100014777047
GO:0009611response to wounding0.00729242213697446
GO:0030500regulation of bone mineralization0.00762495428690688
GO:0046851negative regulation of bone remodeling0.00762495428690688
GO:0051924regulation of calcium ion transport0.00811477290712111
GO:0003044regulation of systemic arterial blood pressure mediated by a chemical signal0.00811477290712111
GO:0042127regulation of cell proliferation0.00840369474061683
GO:0043393regulation of protein binding0.00848023396141709
GO:0045453bone resorption0.00848023396141709
GO:0007041lysosomal transport0.00902583568068267
GO:0043408regulation of MAPKKK cascade0.00934401488107085
GO:0004935adrenoceptor activity0.00934401488107085
GO:0019233sensory perception of pain0.00934401488107085
GO:0042383sarcolemma0.00964137233616056
GO:0003073regulation of systemic arterial blood pressure0.00964137233616056
GO:0045444fat cell differentiation0.00964137233616056
GO:0043269regulation of ion transport0.00991988063841718
GO:0006693prostaglandin metabolic process0.00991988063841718
GO:0006692prostanoid metabolic process0.00991988063841718
GO:0022404molting cycle process0.00997764542160359
GO:0001942hair follicle development0.00997764542160359
GO:0022405hair cycle process0.00997764542160359
GO:0042633hair cycle0.00997764542160359
GO:0042303molting cycle0.00997764542160359
GO:0042311vasodilation0.0101262875003404
GO:0048871multicellular organismal homeostasis0.0101262875003404
GO:0001894tissue homeostasis0.0101262875003404
GO:0030278regulation of ossification0.0101262875003404
GO:0006952defense response0.0102343075644826
GO:0030282bone mineralization0.0102638586560294
GO:0008144drug binding0.0102638586560294
GO:0006940regulation of smooth muscle contraction0.0102638586560294
GO:0040014regulation of multicellular organism growth0.0106775508915968
GO:0045927positive regulation of growth0.0110836621600943
GO:0009605response to external stimulus0.0112791690858978
GO:0044236multicellular organismal metabolic process0.0112791690858978
GO:0007190adenylate cyclase activation0.0112791690858978
GO:0046850regulation of bone remodeling0.0115641987395527
GO:0035264multicellular organism growth0.0115641987395527
GO:0051241negative regulation of multicellular organismal process0.0117116812339498
GO:0031644regulation of neurological process0.0117116812339498
GO:0007034vacuolar transport0.0117116812339498
GO:0051349positive regulation of lyase activity0.0117116812339498
GO:0042562hormone binding0.0117116812339498
GO:0045762positive regulation of adenylate cyclase activity0.0117116812339498
GO:0031281positive regulation of cyclase activity0.0117116812339498
GO:0016599caveolar membrane0.0117116812339498
GO:0005624membrane fraction0.0117867676968731
GO:0051098regulation of binding0.0124093172192136
GO:0005901caveola0.0126493606741491
GO:0009266response to temperature stimulus0.0126493606741491
GO:0051051negative regulation of transport0.0134145121932217
GO:0008283cell proliferation0.0134322515493759
GO:0046456icosanoid biosynthetic process0.0140378287728118
GO:0044255cellular lipid metabolic process0.0140378287728118
GO:0030424axon0.0142643319981669
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.014988085910246
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0152885631121562
GO:0030425dendrite0.0155845405578184
GO:0006937regulation of muscle contraction0.0157602334413733
GO:0006939smooth muscle contraction0.0157602334413733
GO:0016197endosome transport0.0160333098829645
GO:0045761regulation of adenylate cyclase activity0.0160333098829645
GO:0006898receptor-mediated endocytosis0.0160333098829645
GO:0031279regulation of cyclase activity0.0160333098829645
GO:0035150regulation of tube size0.0160333098829645
GO:0050880regulation of blood vessel size0.0160333098829645
GO:0051339regulation of lyase activity0.0160333098829645
GO:0008016regulation of heart contraction0.0160333098829645
GO:0003018vascular process in circulatory system0.0163016636746157
GO:0043176amine binding0.0165663221137575
GO:0008375acetylglucosaminyltransferase activity0.0168273601100729
GO:0000267cell fraction0.0168923916912742
GO:0005783endoplasmic reticulum0.0169249719079181
GO:0003015heart process0.0171107214720378
GO:0060047heart contraction0.0171107214720378
GO:0006629lipid metabolic process0.0178474284798399
GO:0006690icosanoid metabolic process0.0178474284798399
GO:0007219Notch signaling pathway0.0178474284798399
GO:0065008regulation of biological quality0.0179568193605684
GO:0005765lysosomal membrane0.0179714160513918
GO:0030258lipid modification0.0182067513995556
GO:0021700developmental maturation0.0184390856486435
GO:0044424intracellular part0.0190150870897525
GO:0000187activation of MAPK activity0.0195797588639124
GO:0045926negative regulation of growth0.0208195291182241
GO:0005774vacuolar membrane0.0210297736412811
GO:0044437vacuolar part0.0215732462313401
GO:0043406positive regulation of MAP kinase activity0.0219124412563559
GO:0008227amine receptor activity0.0219124412563559
GO:0007519skeletal muscle development0.0219124412563559
GO:0004601peroxidase activity0.0219124412563559
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0219124412563559
GO:0051094positive regulation of developmental process0.0219780875876593
GO:0016324apical plasma membrane0.0219780875876593
GO:0043623cellular protein complex assembly0.0221703307430152
GO:0048523negative regulation of cellular process0.0228002364767809
GO:0048513organ development0.0228235872070181
GO:0006633fatty acid biosynthetic process0.0230480433826354
GO:0044425membrane part0.0234259517225252
GO:0048519negative regulation of biological process0.0240198556243217
GO:0051213dioxygenase activity0.0243764184368213
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0243764184368213
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0245463966944457
GO:0043005neuron projection0.0247144608941831
GO:0006950response to stress0.0249086842099581
GO:0016053organic acid biosynthetic process0.0249088586627779
GO:0046394carboxylic acid biosynthetic process0.0249088586627779
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0249364330664341
GO:0035239tube morphogenesis0.0249364330664341
GO:0045177apical part of cell0.025390642816825
GO:0019933cAMP-mediated signaling0.0254340205500935
GO:0014706striated muscle development0.0254340205500935
GO:0001503ossification0.0254340205500935
GO:0031214biomineral formation0.0254340205500935
GO:0043405regulation of MAP kinase activity0.0267312696456385
GO:0046849bone remodeling0.0274457487539909
GO:0032403protein complex binding0.0287179184066142
GO:0009968negative regulation of signal transduction0.0293936900008597
GO:0051240positive regulation of multicellular organismal process0.0293936900008597
GO:0048771tissue remodeling0.0293936900008597
GO:0043235receptor complex0.0304749358152983
GO:0051049regulation of transport0.0304749358152983
GO:0005622intracellular0.0306441670925344
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.031919692513808
GO:0035295tube development0.031919692513808
GO:0006979response to oxidative stress0.0325711211180107
GO:0019935cyclic-nucleotide-mediated signaling0.0329477699037435
GO:0043231intracellular membrane-bound organelle0.0330240936432405
GO:0043227membrane-bound organelle0.0330240936432405
GO:0051179localization0.0339231025257245
GO:0003008system process0.0339231025257245
GO:0008544epidermis development0.0355591560521856
GO:0008194UDP-glycosyltransferase activity0.0360861562817729
GO:0048731system development0.0360861562817729
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0360861562817729
GO:0045860positive regulation of protein kinase activity0.0364292355072501
GO:0033674positive regulation of kinase activity0.037023933710286
GO:0042165neurotransmitter binding0.0371054595085623
GO:0007398ectoderm development0.0371862005739715
GO:0051347positive regulation of transferase activity0.0372661677579912
GO:0000165MAPKKK cascade0.0378455823254122
GO:0009967positive regulation of signal transduction0.0384194404557652
GO:0042803protein homodimerization activity0.0394830124228228
GO:0005792microsome0.0402899138883853
GO:0003012muscle system process0.0404792835458063
GO:0006936muscle contraction0.0404792835458063
GO:0009628response to abiotic stimulus0.0404792835458063
GO:0042598vesicular fraction0.041266610787076
GO:0007517muscle development0.041805932616859
GO:0006814sodium ion transport0.0418612878776171
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.042445128009613
GO:0043413biopolymer glycosylation0.042445128009613
GO:0016020membrane0.042774578519125
GO:0006816calcium ion transport0.0434886333429926
GO:0006631fatty acid metabolic process0.0451728489267306
GO:0005768endosome0.0454446066848645
GO:0010324membrane invagination0.0459808557273375
GO:0006897endocytosis0.0459808557273375
GO:0004222metalloendopeptidase activity0.0460157287143691
GO:0040008regulation of growth0.0465076206679614
GO:0001501skeletal development0.0481328068956095
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0481579159595137
GO:0048856anatomical structure development0.0485216815438028



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
classical monocyte8.61e-5542
CD14-positive, CD16-negative classical monocyte8.61e-5542
defensive cell8.75e-5148
phagocyte8.75e-5148
myeloid leukocyte1.12e-4872
granulocyte monocyte progenitor cell1.10e-4667
myeloid lineage restricted progenitor cell1.87e-4566
macrophage dendritic cell progenitor1.71e-4161
monopoietic cell3.11e-4159
monocyte3.11e-4159
monoblast3.11e-4159
promonocyte3.11e-4159
leukocyte1.94e-38136
hematopoietic lineage restricted progenitor cell4.26e-34120
nongranular leukocyte4.43e-32115
myeloid cell5.45e-30108
common myeloid progenitor5.45e-30108
hematopoietic stem cell1.38e-29168
angioblastic mesenchymal cell1.38e-29168
hematopoietic cell6.50e-29177
hematopoietic oligopotent progenitor cell3.03e-26161
hematopoietic multipotent progenitor cell3.03e-26161
stuff accumulating cell2.18e-2587
mesenchymal cell5.67e-10354
connective tissue cell9.71e-10361
intermediate monocyte1.56e-089
CD14-positive, CD16-positive monocyte1.56e-089
histamine secreting cell7.88e-085
biogenic amine secreting cell7.88e-085
granulocytopoietic cell7.88e-085
mast cell7.88e-085
mast cell progenitor7.88e-085
basophil mast progenitor cell7.88e-085
motile cell1.66e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.69e-4498
blood island3.69e-4498
bone marrow2.20e-4276
hemolymphoid system1.81e-39108
bone element6.18e-3882
immune system5.53e-3793
skeletal element3.00e-3490
skeletal system5.35e-29100
lateral plate mesoderm2.05e-22203
mesoderm2.86e-14315
mesoderm-derived structure2.86e-14315
presumptive mesoderm2.86e-14315
musculoskeletal system2.95e-11167
connective tissue2.63e-09371


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)
MA0003.10.644804
MA0004.10.221943
MA0006.10.112549
MA0007.10.599001
MA0009.10.621697
MA0014.10.707627
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.11.26611
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.0663643
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.0307766
MA0056.10
MA0057.10.327175
MA0058.10.153757
MA0059.10.15289
MA0060.11.13861
MA0061.10.997605
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.13.14556
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.113.249
MA0074.10.298586
MA0076.11.52428
MA0077.10.586275
MA0078.10.382364
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.176197
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.843378
MA0101.10.372085
MA0103.10.34743
MA0105.11.06659
MA0106.10.33677
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.11.03566
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.10.264652
MA0117.10.656858
MA0119.10.438293
MA0122.10.681203
MA0124.10.810546
MA0125.11.73305
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.934169
MA0140.11.36176
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.231909
MA0145.11.49496
MA0146.10.0662401
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.97018
MA0035.20.740647
MA0039.20.750837
MA0138.20.38342
MA0002.21.07772
MA0137.20.126444
MA0104.20.188874
MA0047.20.326636
MA0112.20.08608
MA0065.20.376744
MA0150.10.508545
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.11.04686
MA0155.10.746636
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.96592
MA0160.10.252705
MA0161.10
MA0162.10.396029
MA0163.10.0944046
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.20.0845756
MA0102.21.14323
MA0258.10.0605489
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


No analysis results for this cluster

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.