Personal tools

Coexpression cluster:C1986

From FANTOM5_SSTAR

Revision as of 17:51, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1986_Preadipocyte_Mesenchymal_basal_Fibroblast_Ewing_hepatic_Adipocyte



Phase1 CAGE Peaks

Hg19::chr7:134464377..134464413,+p1@CALD1
Hg19::chr7:134464414..134464425,+p6@CALD1
Hg19::chr7:134464465..134464476,+p7@CALD1
Hg19::chr7:134655216..134655252,+p42@CALD1
Hg19::chr7:41740181..41740234,-p3@INHBA


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:0048180activin complex0.00274327425429597
GO:0043509activin A complex0.00274327425429597
GO:0043511inhibin complex0.00274327425429597
GO:0043512inhibin A complex0.00274327425429597
GO:0045077negative regulation of interferon-gamma biosynthetic process0.00274327425429597
GO:0045650negative regulation of macrophage differentiation0.00274327425429597
GO:0032278positive regulation of gonadotropin secretion0.00274327425429597
GO:0046881positive regulation of follicle-stimulating hormone secretion0.00274327425429597
GO:0045578negative regulation of B cell differentiation0.00274327425429597
GO:0032276regulation of gonadotropin secretion0.00274327425429597
GO:0046880regulation of follicle-stimulating hormone secretion0.00274327425429597
GO:0046887positive regulation of hormone secretion0.00274327425429597
GO:0048184follistatin binding0.00274327425429597
GO:0046882negative regulation of follicle-stimulating hormone secretion0.00274327425429597
GO:0042541hemoglobin biosynthetic process0.00274327425429597
GO:0045620negative regulation of lymphocyte differentiation0.00274327425429597
GO:0032277negative regulation of gonadotropin secretion0.00274327425429597
GO:0017106activin inhibitor activity0.00274327425429597
GO:0032925regulation of activin receptor signaling pathway0.00274327425429597
GO:0045649regulation of macrophage differentiation0.00274327425429597
GO:0032274gonadotropin secretion0.00274327425429597
GO:0020027hemoglobin metabolic process0.00274327425429597
GO:0032924activin receptor signaling pathway0.00274327425429597
GO:0046884follicle-stimulating hormone secretion0.00274327425429597
GO:0045648positive regulation of erythrocyte differentiation0.00274327425429597
GO:0050869negative regulation of B cell activation0.00316526985601304
GO:0045577regulation of B cell differentiation0.0039187901672028
GO:0017022myosin binding0.0039187901672028
GO:0002762negative regulation of myeloid leukocyte differentiation0.00425655424855442
GO:0030225macrophage differentiation0.00457171996631325
GO:0005160transforming growth factor beta receptor binding0.00457171996631325
GO:0046888negative regulation of hormone secretion0.00457171996631325
GO:0045646regulation of erythrocyte differentiation0.00457171996631325
GO:0045072regulation of interferon-gamma biosynthetic process0.00469189024750552
GO:0042326negative regulation of phosphorylation0.00469189024750552
GO:0045639positive regulation of myeloid cell differentiation0.00469189024750552
GO:0042095interferon-gamma biosynthetic process0.00469189024750552
GO:0045936negative regulation of phosphate metabolic process0.00469189024750552
GO:0002761regulation of myeloid leukocyte differentiation0.00527475089124858
GO:0045619regulation of lymphocyte differentiation0.00535186357924799
GO:0042036negative regulation of cytokine biosynthetic process0.00535186357924799
GO:0051048negative regulation of secretion0.00548549865239052
GO:0001541ovarian follicle development0.00548549865239052
GO:0032609interferon-gamma production0.00548549865239052
GO:0045638negative regulation of myeloid cell differentiation0.00548549865239052
GO:0046883regulation of hormone secretion0.00554377340373417
GO:0051250negative regulation of lymphocyte activation0.00554377340373417
GO:0051047positive regulation of secretion0.00587706040487411
GO:0005523tropomyosin binding0.00587706040487411
GO:0022601menstrual cycle phase0.00658201692404939
GO:0022602menstrual cycle process0.00659246796298695
GO:0050864regulation of B cell activation0.00659246796298695
GO:0008585female gonad development0.0069853226122356
GO:0030183B cell differentiation0.00710061156532613
GO:0046545development of primary female sexual characteristics0.00710061156532613
GO:0046660female sex differentiation0.00710061156532613
GO:0002573myeloid leukocyte differentiation0.0072164862557348
GO:0030218erythrocyte differentiation0.00751867023133696
GO:0042698menstrual cycle0.00751867023133696
GO:0045637regulation of myeloid cell differentiation0.00751867023133696
GO:0000082G1/S transition of mitotic cell cycle0.00751867023133696
GO:0046879hormone secretion0.00751867023133696
GO:0017148negative regulation of translation0.00892179721406047
GO:0031327negative regulation of cellular biosynthetic process0.00963864524147757
GO:0045597positive regulation of cell differentiation0.00991186012605939
GO:0009890negative regulation of biosynthetic process0.0104817334367983
GO:0008406gonad development0.0104817334367983
GO:0048608reproductive structure development0.0104817334367983
GO:0030308negative regulation of cell growth0.0105283196439338
GO:0045792negative regulation of cell size0.010573569048139
GO:0051046regulation of secretion0.0108572593869365
GO:0045137development of primary sexual characteristics0.0108572593869365
GO:0042035regulation of cytokine biosynthetic process0.0108572593869365
GO:0048609reproductive process in a multicellular organism0.0108572593869365
GO:0032504multicellular organism reproduction0.0108572593869365
GO:0042113B cell activation0.0108572593869365
GO:0045926negative regulation of growth0.0108572593869365
GO:0042325regulation of phosphorylation0.0111023468893183
GO:0030098lymphocyte differentiation0.0111023468893183
GO:0045596negative regulation of cell differentiation0.0111239770299129
GO:0042089cytokine biosynthetic process0.0111239770299129
GO:0042107cytokine metabolic process0.0111239770299129
GO:0051094positive regulation of developmental process0.0111239770299129
GO:0051174regulation of phosphorus metabolic process0.0111239770299129
GO:0019220regulation of phosphate metabolic process0.0111239770299129
GO:0003001generation of a signal involved in cell-cell signaling0.0111538065677599
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0117226808852989
GO:0051249regulation of lymphocyte activation0.0117226808852989
GO:0030099myeloid cell differentiation0.0117226808852989
GO:0051093negative regulation of developmental process0.0117226808852989
GO:0050865regulation of cell activation0.0120450365843769
GO:0007548sex differentiation0.0120628609213449
GO:0051329interphase of mitotic cell cycle0.012521706120398
GO:0003006reproductive developmental process0.0126796167943465
GO:0002521leukocyte differentiation0.0128430095254642
GO:0051325interphase0.0128430095254642
GO:0007050cell cycle arrest0.0142618136123162
GO:0051248negative regulation of protein metabolic process0.0145349377240317
GO:0001816cytokine production0.0156311719386937
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.019028151025804
GO:0005516calmodulin binding0.0191102653726784
GO:0045595regulation of cell differentiation0.019324669846072
GO:0046649lymphocyte activation0.0205955677522962
GO:0030097hemopoiesis0.0211016001926894
GO:0001558regulation of cell growth0.0211016001926894
GO:0003012muscle system process0.0211016001926894
GO:0006936muscle contraction0.0211016001926894
GO:0048534hemopoietic or lymphoid organ development0.0219172624202018
GO:0045321leukocyte activation0.0225925424131273
GO:0002520immune system development0.0226352337476506
GO:0006417regulation of translation0.0226771413179177
GO:0031326regulation of cellular biosynthetic process0.0241143574865719
GO:0016049cell growth0.0241143574865719
GO:0040008regulation of growth0.0241143574865719
GO:0008361regulation of cell size0.0243210210561916
GO:0001501skeletal development0.0243210210561916
GO:0001775cell activation0.0243210210561916
GO:0006917induction of apoptosis0.0243210210561916
GO:0012502induction of programmed cell death0.0243210210561916
GO:0032501multicellular organismal process0.0243210210561916
GO:0005179hormone activity0.0243210210561916
GO:0009889regulation of biosynthetic process0.0243210210561916
GO:0045893positive regulation of transcription, DNA-dependent0.0247880963368237
GO:0045786negative regulation of progression through cell cycle0.0248079815534451
GO:0050793regulation of developmental process0.0258084567133596
GO:0008083growth factor activity0.0274410651209666
GO:0043065positive regulation of apoptosis0.0275441036420166
GO:0043068positive regulation of programmed cell death0.0275441036420166
GO:0051239regulation of multicellular organismal process0.0293187191323811
GO:0045941positive regulation of transcription0.0293187191323811
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0301332864785564
GO:0051179localization0.0307047454263562
GO:0007167enzyme linked receptor protein signaling pathway0.0308048393720118
GO:0022414reproductive process0.0310822373624248
GO:0005125cytokine activity0.0313554509768971
GO:0000278mitotic cell cycle0.0327235991619901
GO:0000074regulation of progression through cell cycle0.0351611490324562
GO:0051726regulation of cell cycle0.0354965159760112
GO:0042802identical protein binding0.0355710461104435
GO:0031325positive regulation of cellular metabolic process0.0355710461104435
GO:0022403cell cycle phase0.0357037107339966
GO:0031324negative regulation of cellular metabolic process0.036122093213212
GO:0006928cell motility0.036122093213212
GO:0051674localization of cell0.036122093213212
GO:0046903secretion0.036122093213212
GO:0009893positive regulation of metabolic process0.0365248623183854
GO:0051246regulation of protein metabolic process0.0389616696652158
GO:0006357regulation of transcription from RNA polymerase II promoter0.0389616696652158
GO:0009892negative regulation of metabolic process0.0397965356152556
GO:0003779actin binding0.0397965356152556
GO:0000902cell morphogenesis0.0428340666047415
GO:0032989cellular structure morphogenesis0.0428340666047415
GO:0005615extracellular space0.0469705347814123



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>


Uber Anatomy
Ontology termp-valuen
multi-cellular organism5.51e-19659
organism subdivision8.31e-15365
anatomical system1.20e-14625
somite1.29e-1483
paraxial mesoderm1.29e-1483
presomitic mesoderm1.29e-1483
presumptive segmental plate1.29e-1483
trunk paraxial mesoderm1.29e-1483
presumptive paraxial mesoderm1.29e-1483
splanchnic layer of lateral plate mesoderm1.47e-1484
anatomical group2.61e-14626
vasculature5.36e-1479
vascular system5.36e-1479
muscle tissue1.05e-1263
musculature1.05e-1263
musculature of body1.05e-1263
trunk mesenchyme1.68e-12143
multilaminar epithelium2.02e-1282
dermomyotome4.30e-1270
skeletal muscle tissue5.32e-1261
striated muscle tissue5.32e-1261
myotome5.32e-1261
blood vessel1.97e-1160
epithelial tube open at both ends1.97e-1160
blood vasculature1.97e-1160
vascular cord1.97e-1160
vessel4.38e-1169
multi-tissue structure4.60e-11347
cardiovascular system4.97e-11110
circulatory system1.11e-10113
artery3.24e-1042
arterial blood vessel3.24e-1042
arterial system3.24e-1042
cell layer4.83e-10312
surface structure5.58e-1095
anatomical cluster6.16e-10286
epithelium9.79e-10309
trunk1.36e-09216
embryo1.46e-09612
epithelial tube1.57e-09118
unilaminar epithelium2.04e-09138
embryonic structure3.13e-09605
developing anatomical structure3.13e-09605
germ layer5.55e-09604
embryonic tissue5.55e-09604
presumptive structure5.55e-09604
epiblast (generic)5.55e-09604
systemic artery9.53e-0933
systemic arterial system9.53e-0933
anatomical conduit9.72e-08241
integument1.55e-0745
integumental system1.55e-0745
mesenchyme2.64e-07238
entire embryonic mesenchyme2.64e-07238
skin of body7.39e-0740


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)

{{{tfbs_overrepresentation_jaspar}}}



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.