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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_mean=0

Latest revision as of 18:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:100711801..100711910,-p1@Stat5b
Mm9::chr1:64579555..64579570,+p3@Creb1
Mm9::chr2:22629802..22629818,+p5@Apbb1ip


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

GO IDGO nameFDR corrected p-value
GO:0007595lactation0.000525453577807614
GO:0040018positive regulation of multicellular organism growth0.000541916708159128
GO:0045927positive regulation of growth0.000541916708159128
GO:0040014regulation of multicellular organism growth0.00165668885813224
GO:0035264multicellular organism growth0.0017728978103342
GO:0048609reproductive process in a multicellular organism0.0017728978103342
GO:0032504multicellular organism reproduction0.0017728978103342
GO:0040008regulation of growth0.00677155003102119
GO:0046544development of secondary male sexual characteristics0.00913772318388629
GO:0046543development of secondary female sexual characteristics0.00913772318388629
GO:0022414reproductive process0.00953896831623088
GO:0045136development of secondary sexual characteristics0.00978988128476555
GO:0001553luteinization0.00978988128476555
GO:0042448progesterone metabolic process0.00978988128476555
GO:0001779natural killer cell differentiation0.010749084587409
GO:0045647negative regulation of erythrocyte differentiation0.010749084587409
GO:0045931positive regulation of progression through mitotic cell cycle0.010749084587409
GO:0046887positive regulation of hormone secretion0.0120213437953102
GO:0045579positive regulation of B cell differentiation0.0120213437953102
GO:0045885positive regulation of survival gene product activity0.0137035810317932
GO:0019218regulation of steroid metabolic process0.0145333047197813
GO:0030856regulation of epithelial cell differentiation0.0145333047197813
GO:0042104positive regulation of activated T cell proliferation0.0147318040071788
GO:0045086positive regulation of interleukin-2 biosynthetic process0.0147318040071788
GO:0046006regulation of activated T cell proliferation0.0147318040071788
GO:0045577regulation of B cell differentiation0.0147318040071788
GO:0045646regulation of erythrocyte differentiation0.0147318040071788
GO:0000003reproduction0.0147318040071788
GO:0019915sequestering of lipid0.0147318040071788
GO:0051047positive regulation of secretion0.0147318040071788
GO:0043029T cell homeostasis0.0147318040071788
GO:0045884regulation of survival gene product activity0.015697718401954
GO:0045787positive regulation of progression through cell cycle0.0161165602808381
GO:0030101natural killer cell activation0.0161165602808381
GO:0045076regulation of interleukin-2 biosynthetic process0.0164887251820769
GO:0050798activated T cell proliferation0.0164887251820769
GO:0045621positive regulation of lymphocyte differentiation0.0180221371217239
GO:0042094interleukin-2 biosynthetic process0.0180221371217239
GO:0032623interleukin-2 production0.0182574285122074
GO:0008207C21-steroid hormone metabolic process0.0182574285122074
GO:0050729positive regulation of inflammatory response0.0182574285122074
GO:0031349positive regulation of defense response0.0182574285122074
GO:0021983pituitary gland development0.0182574285122074
GO:0019216regulation of lipid metabolic process0.0182574285122074
GO:0002260lymphocyte homeostasis0.0182574285122074
GO:0045638negative regulation of myeloid cell differentiation0.0182574285122074
GO:0065008regulation of biological quality0.0182574285122074
GO:0021536diencephalon development0.0182574285122074
GO:0046883regulation of hormone secretion0.0182574285122074
GO:0007346regulation of progression through mitotic cell cycle0.0182574285122074
GO:0030879mammary gland development0.0196872254762418
GO:0045619regulation of lymphocyte differentiation0.0201851833574128
GO:0050871positive regulation of B cell activation0.0213388829365318
GO:0001776leukocyte homeostasis0.0213388829365318
GO:0046661male sex differentiation0.0213388829365318
GO:0042102positive regulation of T cell proliferation0.0213388829365318
GO:0007259JAK-STAT cascade0.0213388829365318
GO:0048522positive regulation of cellular process0.0213388829365318
GO:0048872homeostasis of number of cells0.0213388829365318
GO:0031347regulation of defense response0.0213388829365318
GO:0050727regulation of inflammatory response0.0213388829365318
GO:0022601menstrual cycle phase0.0213388829365318
GO:0022602menstrual cycle process0.021723123468064
GO:0042108positive regulation of cytokine biosynthetic process0.0222005142636794
GO:0003700transcription factor activity0.0222005142636794
GO:0045637regulation of myeloid cell differentiation0.0222005142636794
GO:0008585female gonad development0.0222005142636794
GO:0030183B cell differentiation0.0222005142636794
GO:0032946positive regulation of mononuclear cell proliferation0.0222005142636794
GO:0046660female sex differentiation0.0222005142636794
GO:0046545development of primary female sexual characteristics0.0222005142636794
GO:0030855epithelial cell differentiation0.0222005142636794
GO:0050671positive regulation of lymphocyte proliferation0.0222005142636794
GO:0048518positive regulation of biological process0.0222005142636794
GO:0030218erythrocyte differentiation0.0222005142636794
GO:0050864regulation of B cell activation0.0222005142636794
GO:0045727positive regulation of translation0.0233654165316319
GO:0042698menstrual cycle0.0233654165316319
GO:0007565female pregnancy0.0233654165316319
GO:0046879hormone secretion0.0233654165316319
GO:0042129regulation of T cell proliferation0.0236168730883494
GO:0031328positive regulation of cellular biosynthetic process0.0236168730883494
GO:0050870positive regulation of T cell activation0.0236168730883494
GO:0048583regulation of response to stimulus0.023850553830615
GO:0019221cytokine and chemokine mediated signaling pathway0.023850553830615
GO:0030155regulation of cell adhesion0.023850553830615
GO:0035270endocrine system development0.0251440335065073
GO:0042035regulation of cytokine biosynthetic process0.0254182791441992
GO:0008406gonad development0.0254182791441992
GO:0051046regulation of secretion0.0254182791441992
GO:0007154cell communication0.0254182791441992
GO:0032944regulation of mononuclear cell proliferation0.0254182791441992
GO:0009891positive regulation of biosynthetic process0.0254182791441992
GO:0048608reproductive structure development0.0254182791441992
GO:0050670regulation of lymphocyte proliferation0.0254182791441992
GO:0042098T cell proliferation0.026099831366719
GO:0045137development of primary sexual characteristics0.0272352300156898
GO:0042089cytokine biosynthetic process0.0277800589229188
GO:0042107cytokine metabolic process0.0277800589229188
GO:0051251positive regulation of lymphocyte activation0.0277800589229188
GO:0050863regulation of T cell activation0.0284036963151058
GO:0048468cell development0.0286569061337543
GO:0009653anatomical structure morphogenesis0.0286569061337543
GO:0051247positive regulation of protein metabolic process0.0310734952340478
GO:0007548sex differentiation0.0311818288826871
GO:0032943mononuclear cell proliferation0.0311818288826871
GO:0048732gland development0.0311818288826871
GO:0046651lymphocyte proliferation0.0311818288826871
GO:0006916anti-apoptosis0.0325586519314431
GO:0042445hormone metabolic process0.0334980215175915
GO:0051249regulation of lymphocyte activation0.0340101291557644
GO:0042113B cell activation0.0340101291557644
GO:0045596negative regulation of cell differentiation0.0340101291557644
GO:0003006reproductive developmental process0.0340101291557644
GO:0050865regulation of cell activation0.0340101291557644
GO:0003001generation of a signal involved in cell-cell signaling0.0341071241282081
GO:0048513organ development0.035148398214911
GO:0030098lymphocyte differentiation0.035148398214911
GO:0030099myeloid cell differentiation0.035148398214911
GO:0001816cytokine production0.0374931362218485
GO:0030900forebrain development0.0375568027570968
GO:0051093negative regulation of developmental process0.0387304138435095
GO:0008361regulation of cell size0.0395171644779132
GO:0042110T cell activation0.043202129548393
GO:0002009morphogenesis of an epithelium0.044660203493905
GO:0002521leukocyte differentiation0.0457365477392694
GO:0006417regulation of translation0.0467953152711793
GO:0048731system development0.0488320331945464
GO:0031326regulation of cellular biosynthetic process0.0488320331945464
GO:0008202steroid metabolic process0.0488320331945464



Relative expression of the co-expression cluster over median <br>Analyst:




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
hematopoietic system3.12e-1645
blood island3.12e-1645
hemolymphoid system4.54e-1648
immune system4.54e-1648
hemopoietic organ9.17e-1629
immune organ9.17e-1629
thymus1.22e-1423
neck1.22e-1423
respiratory system epithelium1.22e-1423
hemolymphoid system gland1.22e-1423
pharyngeal epithelium1.22e-1423
thymic region1.22e-1423
pharyngeal gland1.22e-1423
entire pharyngeal arch endoderm1.22e-1423
thymus primordium1.22e-1423
early pharyngeal endoderm1.22e-1423
gland of gut1.62e-1424
pharynx3.11e-1324
upper respiratory tract3.11e-1324
chordate pharynx3.11e-1324
pharyngeal arch system3.11e-1324
pharyngeal region of foregut3.11e-1324
mixed endoderm/mesoderm-derived structure1.13e-1135
respiratory system1.15e-1142
respiratory tract1.30e-1141
segment of respiratory tract1.50e-1027
endocrine gland5.38e-1060
lateral plate mesoderm6.76e-1087
foregut1.21e-0980
gland1.49e-0965
endo-epithelium3.71e-0869
craniocervical region7.71e-0836
mesoderm3.10e-07120
mesoderm-derived structure3.10e-07120
presumptive mesoderm3.10e-07120
unilaminar epithelium4.27e-0766
endocrine system7.81e-0772
organ segment8.65e-0735


TFBS overrepresentation<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)
MA0003.11.87396
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.11.6728
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.12.03543
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.12.21145
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.964824
MA0163.11.48428
MA0164.10.933981
MA0080.21.54848
MA0018.20.944669
MA0099.21.06348
MA0079.20.651053
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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