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Latest revision as of 16:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:33947115..33947242,+p1@Lcp2
Mm9::chr1:140071815..140071831,-p2@Ptprc
Mm9::chr6:129187043..129187060,-p@chr6:129187043..129187060
-
Mm9::chr6:129187190..129187197,-p@chr6:129187190..129187197
-
Mm9::chrX:98463521..98463548,-p1@Il2rg
Mm9::chrX:98463557..98463568,-p2@Il2rg


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:0045321leukocyte activation0.000201384263337577
GO:0001775cell activation0.000201384263337577
GO:0050870positive regulation of T cell activation0.00124494442873144
GO:0051251positive regulation of lymphocyte activation0.00134529211205477
GO:0030217T cell differentiation0.00134529211205477
GO:0050863regulation of T cell activation0.00134529211205477
GO:0002376immune system process0.00167704470278518
GO:0051249regulation of lymphocyte activation0.00167704470278518
GO:0050865regulation of cell activation0.00167704470278518
GO:0030098lymphocyte differentiation0.00172823782179823
GO:0042110T cell activation0.0025884242134679
GO:0002521leukocyte differentiation0.00270282578494193
GO:0001915negative regulation of T cell mediated cytotoxicity0.00270282578494193
GO:0009897external side of plasma membrane0.00270282578494193
GO:0009986cell surface0.00323981682805191
GO:0046649lymphocyte activation0.00323981682805191
GO:0001960negative regulation of cytokine and chemokine mediated signaling pathway0.00323981682805191
GO:0045591positive regulation of regulatory T cell differentiation0.00323981682805191
GO:0032831positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation0.00323981682805191
GO:0002361CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation0.00323981682805191
GO:0045589regulation of regulatory T cell differentiation0.00323981682805191
GO:0030097hemopoiesis0.00323981682805191
GO:0048534hemopoietic or lymphoid organ development0.00323981682805191
GO:0019976interleukin-2 binding0.00323981682805191
GO:0001916positive regulation of T cell mediated cytotoxicity0.00323981682805191
GO:0051283negative regulation of sequestering of calcium ion0.00323981682805191
GO:0045066regulatory T cell differentiation0.00323981682805191
GO:0001959regulation of cytokine and chemokine mediated signaling pathway0.00323981682805191
GO:0001914regulation of T cell mediated cytotoxicity0.00323981682805191
GO:0051208sequestering of calcium ion0.00323981682805191
GO:0051238sequestering of metal ion0.00323981682805191
GO:0002711positive regulation of T cell mediated immunity0.00323981682805191
GO:0051282regulation of sequestering of calcium ion0.00323981682805191
GO:0050857positive regulation of antigen receptor-mediated signaling pathway0.00323981682805191
GO:0051209release of sequestered calcium ion into cytosol0.00323981682805191
GO:0002520immune system development0.00352060068852258
GO:0002709regulation of T cell mediated immunity0.00387649149020192
GO:0001911negative regulation of leukocyte mediated cytotoxicity0.00387649149020192
GO:0001913T cell mediated cytotoxicity0.00387649149020192
GO:0051239regulation of multicellular organismal process0.00394701093829918
GO:0050663cytokine secretion0.00553048541377863
GO:0050853B cell receptor signaling pathway0.00629826326499603
GO:0002456T cell mediated immunity0.00703023421918479
GO:0051607defense response to virus0.00772883966084589
GO:0043367CD4-positive, alpha beta T cell differentiation0.00903465807306708
GO:0050854regulation of antigen receptor-mediated signaling pathway0.00903465807306708
GO:0045576mast cell activation0.00925205560095098
GO:0045582positive regulation of T cell differentiation0.00925205560095098
GO:0001912positive regulation of leukocyte mediated cytotoxicity0.00925205560095098
GO:0045621positive regulation of lymphocyte differentiation0.0103017317491084
GO:0002705positive regulation of leukocyte mediated immunity0.0103017317491084
GO:0051235maintenance of localization0.0103017317491084
GO:0001910regulation of leukocyte mediated cytotoxicity0.0103017317491084
GO:0031341regulation of cell killing0.0103017317491084
GO:0002708positive regulation of lymphocyte mediated immunity0.0103017317491084
GO:0002699positive regulation of immune effector process0.0107011816398053
GO:0045580regulation of T cell differentiation0.0107011816398053
GO:0002703regulation of leukocyte mediated immunity0.0107011816398053
GO:0007204elevation of cytosolic calcium ion concentration0.0107011816398053
GO:0002706regulation of lymphocyte mediated immunity0.0107011816398053
GO:0002824positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0109645567172291
GO:0002821positive regulation of adaptive immune response0.0109645567172291
GO:0002697regulation of immune effector process0.0112114061902319
GO:0051480cytosolic calcium ion homeostasis0.0112114061902319
GO:0046632alpha-beta T cell differentiation0.0120389508307953
GO:0001906cell killing0.0120389508307953
GO:0002819regulation of adaptive immune response0.0120389508307953
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.0120389508307953
GO:0001909leukocyte mediated cytotoxicity0.0120389508307953
GO:0045619regulation of lymphocyte differentiation0.0124056933686874
GO:0042102positive regulation of T cell proliferation0.0135893450616824
GO:0002274myeloid leukocyte activation0.0135893450616824
GO:0050851antigen receptor-mediated signaling pathway0.0135893450616824
GO:0042100B cell proliferation0.0135893450616824
GO:0005925focal adhesion0.0135893450616824
GO:0009306protein secretion0.0148981474371567
GO:0005924cell-substrate adherens junction0.0149991928481333
GO:0046631alpha-beta T cell activation0.0149991928481333
GO:0002429immune response-activating cell surface receptor signaling pathway0.01528621194509
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0154348204545951
GO:0030055cell-matrix junction0.0154348204545951
GO:0030183B cell differentiation0.0154348204545951
GO:0019965interleukin binding0.0154348204545951
GO:0002757immune response-activating signal transduction0.0154348204545951
GO:0032946positive regulation of mononuclear cell proliferation0.0154348204545951
GO:0006469negative regulation of protein kinase activity0.0154348204545951
GO:0033673negative regulation of kinase activity0.0154348204545951
GO:0050671positive regulation of lymphocyte proliferation0.0154348204545951
GO:0051348negative regulation of transferase activity0.0159285124615529
GO:0002764immune response-regulating signal transduction0.0159285124615529
GO:0042129regulation of T cell proliferation0.0174079160485435
GO:0019221cytokine and chemokine mediated signaling pathway0.0184455722071303
GO:0043086negative regulation of catalytic activity0.0190561308588889
GO:0019901protein kinase binding0.019244074682621
GO:0019838growth factor binding0.019244074682621
GO:0009615response to virus0.019244074682621
GO:0019900kinase binding0.0194333038375189
GO:0050670regulation of lymphocyte proliferation0.0201798342889598
GO:0032944regulation of mononuclear cell proliferation0.0201798342889598
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0203538637423428
GO:0042098T cell proliferation0.0205244061748399
GO:0006874cellular calcium ion homeostasis0.0217964541555786
GO:0005912adherens junction0.0220995211409495
GO:0055074calcium ion homeostasis0.0220995211409495
GO:0032501multicellular organismal process0.0222698414508014
GO:0006875cellular metal ion homeostasis0.0234533739515075
GO:0019955cytokine binding0.0235849228369584
GO:0055065metal ion homeostasis0.0237139974166393
GO:0016323basolateral plasma membrane0.0241848559177353
GO:0032943mononuclear cell proliferation0.0251006750095906
GO:0046651lymphocyte proliferation0.0251006750095906
GO:0002253activation of immune response0.0258808109738987
GO:0042113B cell activation0.0283044698039734
GO:0004725protein tyrosine phosphatase activity0.0283847001189565
GO:0002250adaptive immune response0.0288636487410764
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0288636487410764
GO:0009968negative regulation of signal transduction0.0289369016177656
GO:0048513organ development0.0290796100339192
GO:0002449lymphocyte mediated immunity0.0290796100339192
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0297727236658622
GO:0050778positive regulation of immune response0.0297787211431084
GO:0055066di-, tri-valent inorganic cation homeostasis0.0297787211431084
GO:0002684positive regulation of immune system process0.0297787211431084
GO:0002443leukocyte mediated immunity0.0297787211431084
GO:0001816cytokine production0.0297787211431084
GO:0030003cellular cation homeostasis0.0310259053456914
GO:0006470protein amino acid dephosphorylation0.0313701166319096
GO:0055080cation homeostasis0.0314169453428553
GO:0050776regulation of immune response0.0321720903223131
GO:0044459plasma membrane part0.0321720903223131
GO:0002682regulation of immune system process0.0324081502288187
GO:0051240positive regulation of multicellular organismal process0.0332938216522709
GO:0016311dephosphorylation0.0333240854308479
GO:0045859regulation of protein kinase activity0.0355805098648134
GO:0006917induction of apoptosis0.0356054391453159
GO:0012502induction of programmed cell death0.0356054391453159
GO:0043549regulation of kinase activity0.0361615764838792
GO:0019899enzyme binding0.0361695157330812
GO:0002252immune effector process0.0361849658594344
GO:0051338regulation of transferase activity0.0361849658594344
GO:0048731system development0.0368141696897198
GO:0004721phosphoprotein phosphatase activity0.0375024831801309
GO:0048869cellular developmental process0.0375024831801309
GO:0030154cell differentiation0.0375024831801309
GO:0055082cellular chemical homeostasis0.0375024831801309
GO:0006873cellular ion homeostasis0.0375024831801309
GO:0043065positive regulation of apoptosis0.0414571660600049
GO:0051707response to other organism0.0414571660600049
GO:0043068positive regulation of programmed cell death0.0414571660600049
GO:0050801ion homeostasis0.0414571660600049
GO:0008284positive regulation of cell proliferation0.0436395050356169
GO:0005886plasma membrane0.0453843086993348
GO:0048856anatomical structure development0.0456400827179775



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
hemolymphoid system3.03e-1948
immune system3.03e-1948
hematopoietic system7.50e-1845
blood island7.50e-1845
lateral plate mesoderm3.82e-1487
hemopoietic organ4.02e-1229
immune organ4.02e-1229
mixed endoderm/mesoderm-derived structure1.79e-1135
foregut4.31e-1080
mesoderm5.81e-10120
mesoderm-derived structure5.81e-10120
presumptive mesoderm5.81e-10120
gland of gut1.42e-0924
thymus2.35e-0923
neck2.35e-0923
respiratory system epithelium2.35e-0923
hemolymphoid system gland2.35e-0923
pharyngeal epithelium2.35e-0923
thymic region2.35e-0923
pharyngeal gland2.35e-0923
entire pharyngeal arch endoderm2.35e-0923
thymus primordium2.35e-0923
early pharyngeal endoderm2.35e-0923
pharynx4.96e-0924
upper respiratory tract4.96e-0924
chordate pharynx4.96e-0924
pharyngeal arch system4.96e-0924
pharyngeal region of foregut4.96e-0924
respiratory system6.47e-0942
respiratory tract1.12e-0841
endoderm-derived structure6.48e-08118
endoderm6.48e-08118
presumptive endoderm6.48e-08118
digestive system1.03e-07116
digestive tract1.03e-07116
primitive gut1.03e-07116
subdivision of digestive tract3.21e-07114
organism subdivision9.99e-07150


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)
MA0003.10.00973143
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.11.22706
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.757042
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.11.46111
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.12.84212
MA0074.10.638014
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.11.19271
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.11.58388
MA0139.10.243463
MA0140.10.625902
MA0141.11.07584
MA0142.12.03291
MA0143.11.72325
MA0144.10.829535
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.21.11803
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.132921
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.20.0267793
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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