MCL coexpression mm9:1643: Difference between revisions
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{{MCL_coexpression_mm9 | 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membrane;0.0111713463617682;14998!GO:0044440;endosomal part;0.0111713463617682;14998!GO:0006955;immune response;0.0111713463617682;14998,17084!GO:0005765;lysosomal membrane;0.0111713463617682;14998!GO:0045059;positive thymic T cell selection;0.0111713463617682;14998!GO:0043368;positive T cell selection;0.0111713463617682;14998!GO:0005771;multivesicular body;0.0111713463617682;14998!GO:0042613;MHC class II protein complex;0.0111713463617682;14998!GO:0045582;positive regulation of T cell differentiation;0.0111713463617682;14998!GO:0051085;chaperone cofactor-dependent protein folding;0.0111713463617682;14998!GO:0045061;thymic T cell selection;0.0111713463617682;14998!GO:0006458;'de novo' protein folding;0.0111713463617682;14998!GO:0051084;'de novo' posttranslational protein folding;0.0111713463617682;14998!GO:0002376;immune system process;0.0111713463617682;14998,17084!GO:0045621;positive regulation of lymphocyte differentiation;0.0111713463617682;14998!GO:0002495;antigen processing and presentation of peptide antigen via MHC class II;0.0111713463617682;14998!GO:0005774;vacuolar membrane;0.0111713463617682;14998!GO:0019886;antigen processing and presentation of exogenous peptide antigen via MHC class II;0.0111713463617682;14998!GO:0045580;regulation of T cell differentiation;0.0111713463617682;14998!GO:0045058;T cell selection;0.0111713463617682;14998!GO:0002478;antigen processing and presentation of exogenous peptide antigen;0.0112649144841956;14998!GO:0002504;antigen processing and presentation of peptide or polysaccharide antigen via MHC class II;0.0113499436687616;14998!GO:0044437;vacuolar part;0.0114275476899699;14998!GO:0045619;regulation of lymphocyte differentiation;0.0120893513204155;14998!GO:0019884;antigen processing and presentation of exogenous antigen;0.0120893513204155;14998!GO:0033077;T cell differentiation in the thymus;0.0126344989165626;14998!GO:0005770;late endosome;0.0126699028249458;14998!GO:0042611;MHC protein complex;0.0126699028249458;14998!GO:0048002;antigen processing and presentation of peptide antigen;0.0154015745624465;14998!GO:0050870;positive regulation of T cell activation;0.018824533378516;14998!GO:0019882;antigen processing and presentation;0.0241392290912958;14998!GO:0051251;positive regulation of lymphocyte activation;0.0242648977314301;14998!GO:0030217;T cell differentiation;0.0242648977314301;14998!GO:0050863;regulation of T cell activation;0.0243220607194743;14998!GO:0016064;immunoglobulin mediated immune response;0.0258820835066117;14998!GO:0019724;B cell mediated immunity;0.0258820835066117;14998!GO:0051249;regulation of lymphocyte activation;0.0282219397142;14998!GO:0050865;regulation of cell activation;0.0282219397142;14998!GO:0002460;adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains;0.0282219397142;14998!GO:0002250;adaptive immune response;0.0282219397142;14998!GO:0030098;lymphocyte differentiation;0.0282219397142;14998!GO:0002449;lymphocyte mediated immunity;0.0282219397142;14998!GO:0050778;positive regulation of immune response;0.0282219397142;14998!GO:0002684;positive regulation of immune system process;0.0282219397142;14998!GO:0005886;plasma membrane;0.0282219397142;14998,17084!GO:0002443;leukocyte mediated immunity;0.0282219397142;14998!GO:0050776;regulation of immune response;0.0308588446470944;14998!GO:0002682;regulation of immune system process;0.0308588446470944;14998!GO:0051240;positive regulation of multicellular organismal process;0.0309310587511431;14998!GO:0042110;T cell activation;0.0309310587511431;14998!GO:0006461;protein complex assembly;0.0320018973692504;14998!GO:0002521;leukocyte differentiation;0.0320018973692504;14998!GO:0006457;protein folding;0.0321371246181744;14998!GO:0002252;immune effector process;0.0327506438198464;14998!GO:0005768;endosome;0.0390333443011157;14998!GO:0005764;lysosome;0.0390333443011157;14998!GO:0000323;lytic vacuole;0.0390333443011157;14998!GO:0046649;lymphocyte activation;0.0423440093609866;14998!GO:0005773;vacuole;0.0423440093609866;14998!GO:0045321;leukocyte activation;0.0438610383771851;14998!GO:0030097;hemopoiesis;0.0438610383771851;14998!GO:0006954;inflammatory response;0.0438610383771851;17084!GO:0001775;cell activation;0.0458462073904284;14998!GO:0048534;hemopoietic or lymphoid organ development;0.0473617803066281;14998!|ontology_enrichment_celltype=CL:0000049!1.32e-07!19|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002371!2.96e-11!16;UBERON:0001474!3.55e-11!22;UBERON:0004765!3.55e-11!22;UBERON:0001434!3.55e-11!22;UBERON:0002193!1.09e-09!48;UBERON:0002405!1.09e-09!48;UBERON:0007023!3.05e-08!51;UBERON:0002390!3.53e-08!45;UBERON:0003061!3.53e-08!45;UBERON:0002204!3.40e-07!32|tfbs_overrepresentation_for_novel_motifs=2.35102,0.612204,0.529553,0.603273,1.04755,0.618805,0.715644,0.812379,0.310789,0.370407,0.668936,0.702872,0.812978,0.728641,1.0876,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,1.38127,0.641282,0.456327,1.20535,0.626183,1.03545,0.395107,0.253145,0.425309,0.791367,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,1.58288,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,1.74061,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,1.49829,2.78941,1.23259,0.257421,1.27178,0.253065,0.835925,0.997094,0.494135,1.50308,0.948899,0.794502,0.293164,1.1148,0.0793594,1.03552,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,1.06179,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,1.23125,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,1.39156,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,3.34092,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167|tfbs_overrepresentation_jaspar=MA0003.1;0.211284,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.0502051,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;1.7574,MA0050.1;1.55615,MA0051.1;1.80893,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.192781,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.881183,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.000589538,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;1.45902,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.476962,MA0146.1;0.21827,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.140205,MA0138.2;0.861035,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.47695,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.515751,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.0699535,MA0163.1;0.497328,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.0381166,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0}} | ||
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| |||
| | |||
}} | |||
Latest revision as of 17:16, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr13:37437253..37437276,+ | p2@Ly86 |
| Mm9::chr13:37437284..37437301,+ | p1@Ly86 |
| Mm9::chr17:34272526..34272616,+ | p1@H2-DMa |
| Mm9::chr19:44463324..44463335,+ | p@chr19:44463324..44463335 + |
| Mm9::chr7:100027264..100027271,- | p@chr7:100027264..100027271 - |
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0010008 | endosome membrane | 0.0111713463617682 |
| GO:0044440 | endosomal part | 0.0111713463617682 |
| GO:0006955 | immune response | 0.0111713463617682 |
| GO:0005765 | lysosomal membrane | 0.0111713463617682 |
| GO:0045059 | positive thymic T cell selection | 0.0111713463617682 |
| GO:0043368 | positive T cell selection | 0.0111713463617682 |
| GO:0005771 | multivesicular body | 0.0111713463617682 |
| GO:0042613 | MHC class II protein complex | 0.0111713463617682 |
| GO:0045582 | positive regulation of T cell differentiation | 0.0111713463617682 |
| GO:0051085 | chaperone cofactor-dependent protein folding | 0.0111713463617682 |
| GO:0045061 | thymic T cell selection | 0.0111713463617682 |
| GO:0006458 | 'de novo' protein folding | 0.0111713463617682 |
| GO:0051084 | 'de novo' posttranslational protein folding | 0.0111713463617682 |
| GO:0002376 | immune system process | 0.0111713463617682 |
| GO:0045621 | positive regulation of lymphocyte differentiation | 0.0111713463617682 |
| GO:0002495 | antigen processing and presentation of peptide antigen via MHC class II | 0.0111713463617682 |
| GO:0005774 | vacuolar membrane | 0.0111713463617682 |
| GO:0019886 | antigen processing and presentation of exogenous peptide antigen via MHC class II | 0.0111713463617682 |
| GO:0045580 | regulation of T cell differentiation | 0.0111713463617682 |
| GO:0045058 | T cell selection | 0.0111713463617682 |
| GO:0002478 | antigen processing and presentation of exogenous peptide antigen | 0.0112649144841956 |
| GO:0002504 | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 0.0113499436687616 |
| GO:0044437 | vacuolar part | 0.0114275476899699 |
| GO:0045619 | regulation of lymphocyte differentiation | 0.0120893513204155 |
| GO:0019884 | antigen processing and presentation of exogenous antigen | 0.0120893513204155 |
| GO:0033077 | T cell differentiation in the thymus | 0.0126344989165626 |
| GO:0005770 | late endosome | 0.0126699028249458 |
| GO:0042611 | MHC protein complex | 0.0126699028249458 |
| GO:0048002 | antigen processing and presentation of peptide antigen | 0.0154015745624465 |
| GO:0050870 | positive regulation of T cell activation | 0.018824533378516 |
| GO:0019882 | antigen processing and presentation | 0.0241392290912958 |
| GO:0051251 | positive regulation of lymphocyte activation | 0.0242648977314301 |
| GO:0030217 | T cell differentiation | 0.0242648977314301 |
| GO:0050863 | regulation of T cell activation | 0.0243220607194743 |
| GO:0016064 | immunoglobulin mediated immune response | 0.0258820835066117 |
| GO:0019724 | B cell mediated immunity | 0.0258820835066117 |
| GO:0051249 | regulation of lymphocyte activation | 0.0282219397142 |
| GO:0050865 | regulation of cell activation | 0.0282219397142 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.0282219397142 |
| GO:0002250 | adaptive immune response | 0.0282219397142 |
| GO:0030098 | lymphocyte differentiation | 0.0282219397142 |
| GO:0002449 | lymphocyte mediated immunity | 0.0282219397142 |
| GO:0050778 | positive regulation of immune response | 0.0282219397142 |
| GO:0002684 | positive regulation of immune system process | 0.0282219397142 |
| GO:0005886 | plasma membrane | 0.0282219397142 |
| GO:0002443 | leukocyte mediated immunity | 0.0282219397142 |
| GO:0050776 | regulation of immune response | 0.0308588446470944 |
| GO:0002682 | regulation of immune system process | 0.0308588446470944 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.0309310587511431 |
| GO:0042110 | T cell activation | 0.0309310587511431 |
| GO:0006461 | protein complex assembly | 0.0320018973692504 |
| GO:0002521 | leukocyte differentiation | 0.0320018973692504 |
| GO:0006457 | protein folding | 0.0321371246181744 |
| GO:0002252 | immune effector process | 0.0327506438198464 |
| GO:0005768 | endosome | 0.0390333443011157 |
| GO:0005764 | lysosome | 0.0390333443011157 |
| GO:0000323 | lytic vacuole | 0.0390333443011157 |
| GO:0046649 | lymphocyte activation | 0.0423440093609866 |
| GO:0005773 | vacuole | 0.0423440093609866 |
| GO:0045321 | leukocyte activation | 0.0438610383771851 |
| GO:0030097 | hemopoiesis | 0.0438610383771851 |
| GO:0006954 | inflammatory response | 0.0438610383771851 |
| GO:0001775 | cell activation | 0.0458462073904284 |
| GO:0048534 | hemopoietic or lymphoid organ development | 0.0473617803066281 |
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>
| Ontology term | p-value | n |
|---|---|---|
| common myeloid progenitor | 1.32e-07 | 19 |
| Ontology term | p-value | n |
|---|---|---|
| bone marrow | 2.96e-11 | 16 |
| bone element | 3.55e-11 | 22 |
| skeletal element | 3.55e-11 | 22 |
| skeletal system | 3.55e-11 | 22 |
| hemolymphoid system | 1.09e-09 | 48 |
| immune system | 1.09e-09 | 48 |
| adult organism | 3.05e-08 | 51 |
| hematopoietic system | 3.53e-08 | 45 |
| blood island | 3.53e-08 | 45 |
| musculoskeletal system | 3.40e-07 | 32 |
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) |
|---|---|
| MA0003.1 | 0.211284 |
| MA0004.1 | 0.603793 |
| MA0006.1 | 0.419915 |
| MA0007.1 | 0.587678 |
| MA0009.1 | 1.06266 |
| MA0014.1 | 0.0502051 |
| MA0017.1 | 0.449113 |
| MA0019.1 | 0.874061 |
| MA0024.1 | 1.01759 |
| MA0025.1 | 1.30092 |
| MA0027.1 | 2.72141 |
| MA0028.1 | 0.43138 |
| MA0029.1 | 0.995171 |
| MA0030.1 | 1.00195 |
| MA0031.1 | 0.965177 |
| MA0038.1 | 0.757669 |
| MA0040.1 | 1.07552 |
| MA0041.1 | 0.522007 |
| MA0042.1 | 0.507715 |
| MA0043.1 | 1.1618 |
| MA0046.1 | 1.09955 |
| MA0048.1 | 1.7574 |
| MA0050.1 | 1.55615 |
| MA0051.1 | 1.80893 |
| MA0052.1 | 1.08379 |
| MA0055.1 | 0.0851423 |
| MA0056.1 | 0 |
| MA0057.1 | 0.192781 |
| MA0058.1 | 0.50032 |
| MA0059.1 | 0.513699 |
| MA0060.1 | 0.881183 |
| MA0061.1 | 0.364227 |
| MA0063.1 | 0 |
| MA0066.1 | 0.746072 |
| MA0067.1 | 1.41352 |
| MA0068.1 | 0.197245 |
| MA0069.1 | 1.08414 |
| MA0070.1 | 1.07418 |
| MA0071.1 | 0.644448 |
| MA0072.1 | 1.06547 |
| MA0073.1 | 0.000589538 |
| MA0074.1 | 0.708108 |
| MA0076.1 | 0.470037 |
| MA0077.1 | 1.04318 |
| MA0078.1 | 0.801834 |
| MA0081.1 | 0.53877 |
| MA0083.1 | 1.16099 |
| MA0084.1 | 1.74401 |
| MA0087.1 | 1.11687 |
| MA0088.1 | 0.148348 |
| MA0089.1 | 0 |
| MA0090.1 | 0.566938 |
| MA0091.1 | 0.617887 |
| MA0092.1 | 0.567278 |
| MA0093.1 | 0.440484 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.695835 |
| MA0101.1 | 0.523409 |
| MA0103.1 | 0.460936 |
| MA0105.1 | 0.248108 |
| MA0106.1 | 0.809991 |
| MA0107.1 | 0.454197 |
| MA0108.2 | 0.897859 |
| MA0109.1 | 0 |
| MA0111.1 | 0.582193 |
| MA0113.1 | 0.780358 |
| MA0114.1 | 0.361633 |
| MA0115.1 | 1.16466 |
| MA0116.1 | 0.419688 |
| MA0117.1 | 1.13165 |
| MA0119.1 | 0.524046 |
| MA0122.1 | 1.15196 |
| MA0124.1 | 1.35963 |
| MA0125.1 | 1.28445 |
| MA0130.1 | 0 |
| MA0131.1 | 0.869325 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.19898 |
| MA0136.1 | 0.729175 |
| MA0139.1 | 1.45902 |
| MA0140.1 | 0.695713 |
| MA0141.1 | 0.482463 |
| MA0142.1 | 0.950155 |
| MA0143.1 | 0.797553 |
| MA0144.1 | 0.365053 |
| MA0145.1 | 0.476962 |
| MA0146.1 | 0.21827 |
| MA0147.1 | 0.378658 |
| MA0148.1 | 0.621195 |
| MA0149.1 | 0.529387 |
| MA0062.2 | 0.254018 |
| MA0035.2 | 0.700704 |
| MA0039.2 | 0.140205 |
| MA0138.2 | 0.861035 |
| MA0002.2 | 0.809945 |
| MA0137.2 | 0.479301 |
| MA0104.2 | 0.315156 |
| MA0047.2 | 0.75686 |
| MA0112.2 | 0.47695 |
| MA0065.2 | 0.158101 |
| MA0150.1 | 0.587557 |
| MA0151.1 | 0 |
| MA0152.1 | 0.756973 |
| MA0153.1 | 1.21594 |
| MA0154.1 | 0.203217 |
| MA0155.1 | 0.515751 |
| MA0156.1 | 0.469089 |
| MA0157.1 | 0.91689 |
| MA0158.1 | 0 |
| MA0159.1 | 0.389847 |
| MA0160.1 | 0.624415 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0699535 |
| MA0163.1 | 0.497328 |
| MA0164.1 | 0.729558 |
| MA0080.2 | 0.455167 |
| MA0018.2 | 0.739807 |
| MA0099.2 | 0.854449 |
| MA0079.2 | 0.0381166 |
| MA0102.2 | 1.79669 |
| MA0258.1 | 0.346619 |
| MA0259.1 | 0.366802 |
| MA0442.1 | 0 |
