MCL coexpression mm9:671: Difference between revisions
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{{MCL_coexpression_mm9| | 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nervous system development;0.000483665690904929;65100,22772,22771!GO:0001843;neural tube closure;0.000498947244351965;65100,22772!GO:0014020;primary neural tube formation;0.000498947244351965;65100,22772!GO:0001841;neural tube formation;0.000498947244351965;65100,22772!GO:0001839;neural plate morphogenesis;0.000498947244351965;65100,22772!GO:0001838;embryonic epithelial tube formation;0.000498947244351965;65100,22772!GO:0001840;neural plate development;0.000498947244351965;65100,22772!GO:0021915;neural tube development;0.000568641857073429;65100,22772!GO:0016331;morphogenesis of embryonic epithelium;0.000636282393872113;65100,22772!GO:0003677;DNA binding;0.000636282393872113;65100,22772,22771,22774!GO:0007399;nervous system development;0.000835223444455235;65100,22772,22771!GO:0002009;morphogenesis of an epithelium;0.00136167516678533;65100,22772!GO:0035239;tube morphogenesis;0.00181898416272182;65100,22772!GO:0003676;nucleic acid binding;0.00213504303258981;65100,22772,22771,22774!GO:0007420;brain development;0.00243345122482529;65100,22771!GO:0048598;embryonic morphogenesis;0.00256023272294392;65100,22772!GO:0035295;tube development;0.00256023272294392;65100,22772!GO:0016337;cell-cell adhesion;0.0025884509832289;65100,22772!GO:0043009;chordate embryonic development;0.00269954463698739;65100,22772!GO:0009792;embryonic development ending in birth or egg hatching;0.00269954463698739;65100,22772!GO:0005634;nucleus;0.00625387709903602;65100,22772,22771,22774!GO:0008589;regulation of smoothened signaling pathway;0.00703697243384536;22771!GO:0048731;system development;0.00703697243384536;65100,22772,22771!GO:0048869;cellular developmental process;0.00703697243384536;65100,22772,22771!GO:0030154;cell differentiation;0.00703697243384536;65100,22772,22771!GO:0009790;embryonic development;0.00815239420749265;65100,22772!GO:0008270;zinc ion binding;0.0084646283988294;22772,22771,22774!GO:0048856;anatomical structure development;0.00910520032603384;65100,22772,22771!GO:0007275;multicellular organismal development;0.0116707777989934;65100,22772,22771!GO:0022610;biological adhesion;0.0116707777989934;65100,22772!GO:0007155;cell adhesion;0.0116707777989934;65100,22772!GO:0007224;smoothened signaling pathway;0.0116707777989934;22771!GO:0048066;pigmentation during development;0.0117203371206961;22772!GO:0046914;transition metal ion binding;0.0125989430938281;22772,22771,22774!GO:0032502;developmental process;0.0221024338513604;65100,22772,22771!GO:0043231;intracellular membrane-bound organelle;0.0221024338513604;65100,22772,22771,22774!GO:0043227;membrane-bound organelle;0.0221024338513604;65100,22772,22771,22774!GO:0043169;cation binding;0.0288932550287507;22772,22771,22774!GO:0009653;anatomical structure morphogenesis;0.0318776641924248;65100,22772!GO:0030900;forebrain development;0.0319765146532927;65100!GO:0043229;intracellular organelle;0.0319765146532927;65100,22772,22771,22774!GO:0043226;organelle;0.0319765146532927;65100,22772,22771,22774!GO:0046872;metal ion binding;0.0322470960645324;22772,22771,22774!GO:0043167;ion binding;0.0334005799442731;22772,22771,22774!GO:0048513;organ development;0.0386898252973023;65100,22771!GO:0032501;multicellular organismal process;0.045169113728162;65100,22772,22771!|ontology_enrichment_celltype=CL:0000117!6.87e-13!23;CL:0000337!6.87e-13!23;CL:0002319!5.12e-11!43;CL:0000221!1.38e-10!44;CL:0000133!1.38e-10!44;CL:0000055!1.02e-08!49;CL:0000540!4.62e-08!33;CL:0000047!4.62e-08!33;CL:0000031!4.62e-08!33;CL:0000404!4.62e-08!33|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002346!9.21e-20!64;UBERON:0003075!9.21e-20!64;UBERON:0007284!9.21e-20!64;UBERON:0001017!1.74e-19!73;UBERON:0001016!1.39e-18!75;UBERON:0000073!1.70e-18!54;UBERON:0001049!6.46e-18!52;UBERON:0005068!6.46e-18!52;UBERON:0006241!6.46e-18!52;UBERON:0007135!6.46e-18!52;UBERON:0004121!8.68e-18!95;UBERON:0000924!8.68e-18!95;UBERON:0006601!8.68e-18!95;UBERON:0010371!1.56e-16!73;UBERON:0002616!5.02e-13!46;UBERON:0003056!1.09e-12!49;UBERON:0000955!1.48e-12!47;UBERON:0006238!1.48e-12!47;UBERON:0003076!1.09e-10!12;UBERON:0003057!1.09e-10!12;UBERON:0010314!1.82e-10!92;UBERON:0003080!1.27e-09!40;UBERON:0002780!3.11e-09!39;UBERON:0001890!3.11e-09!39;UBERON:0006240!3.11e-09!39;UBERON:0002020!2.05e-08!34;UBERON:0002240!4.56e-07!6;UBERON:0005174!4.56e-07!6;UBERON:0001137!4.56e-07!6;UBERON:0001948!9.34e-07!5;UBERON:0002315!9.34e-07!5|tfbs_overrepresentation_for_novel_motifs=0.29262,0.750994,0.269904,0.329881,0.52369,0.342839,0.425757,0.106126,0.362206,0.081847,0.385334,0.414631,0.345518,0.437133,0.189961,0,0.619876,0.508485,0.656134,0.688036,0.238546,0.281622,1.11256,0.520732,0.276437,0.4628,0.0908349,0.361771,0.611503,0.0650265,0.349031,0.717576,1.54849,0.270473,0.19035,3.48339,0.486454,1.0583,0.445168,1.85421,0.173534,0.353696,0.478787,0.191571,0.557517,0.319944,0.543674,0.376103,0.401883,0.215702,1.4677,0.488021,0.479906,1.99116,0.87275,0.443782,0.634658,1.03993,0.288386,0.441884,0.698157,1.24284,0.383763,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.720972,0.0307733,0.905636,0.0810502,1.39651,0.0786324,0.532872,0.681539,0.242107,0.110993,0.636582,0.495545,0.333618,0.792744,1.32338,4.44159,4.38346,1.3522,1.51408,1.07554,0.797601,0.730003,0.535058,1.38871,0.129056,0.340672,0.732731,0.543917,0.197581,0.486605,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.688705,0.240055,0.781068,0.840348,0.243062,0.390066,1.0825,0.172131,0.170188,0.886406,0.621127,0.931584,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,1.10612,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,19.1927,0.300001,0.934673,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.60254,0.871497,0.103135,0.857198,0.133365,0.455644,0.93735,0.488969,0.199652,0.790184,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,1.13944,1.50123,0.413167,0.0207556|tfbs_overrepresentation_jaspar=MA0003.1;0.261277,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.144697,MA0017.1;0.598706,MA0019.1;0.567591,MA0024.1;1.6716,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.440822,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;2.71747,MA0056.1;0,MA0057.1;2.63634,MA0058.1;0.246908,MA0059.1;0.714494,MA0060.1;0.395347,MA0061.1;0.884293,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.187364,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;8.00317,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;1.39097,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.28966,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.216742,MA0105.1;1.95127,MA0106.1;1.26962,MA0107.1;0.607721,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.446898,MA0115.1;0.84036,MA0116.1;0.546914,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.103495,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.57264,MA0146.1;1.40012,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.0791588,MA0035.2;0.412747,MA0039.2;0.0387728,MA0138.2;0.555696,MA0002.2;0.343346,MA0137.2;0.230686,MA0104.2;0.11535,MA0047.2;0.46201,MA0112.2;0.57262,MA0065.2;0.314773,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;1.16232,MA0155.1;0.637282,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;1.19805,MA0163.1;0.355774,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;1.59098,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.14914,MA0442.1;0}} | ||
Latest revision as of 15:42, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr14:122864041..122864099,- | p@chr14:122864041..122864099 - |
| Mm9::chr14:122864676..122864708,- | p1@Zic5 |
| Mm9::chr14:122873661..122873686,+ | p@chr14:122873661..122873686 + |
| Mm9::chr14:122873694..122873710,+ | p@chr14:122873694..122873710 + |
| Mm9::chr14:122879279..122879285,+ | p@chr14:122879279..122879285 + |
| Mm9::chr9:91259711..91259725,- | p@chr9:91259711..91259725 - |
| Mm9::chr9:91260248..91260259,- | p4@Zic1 |
| Mm9::chr9:91262990..91263011,- | p@chr9:91262990..91263011 - |
| Mm9::chr9:91263173..91263220,+ | p2@Zic4 |
| Mm9::chr9:91273474..91273484,+ | p11@Zic4 |
| Mm9::chr9:91275527..91275544,+ | p@chr9:91275527..91275544 + |
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:0007417 | central nervous system development | 0.000483665690904929 |
| GO:0001843 | neural tube closure | 0.000498947244351965 |
| GO:0014020 | primary neural tube formation | 0.000498947244351965 |
| GO:0001841 | neural tube formation | 0.000498947244351965 |
| GO:0001839 | neural plate morphogenesis | 0.000498947244351965 |
| GO:0001838 | embryonic epithelial tube formation | 0.000498947244351965 |
| GO:0001840 | neural plate development | 0.000498947244351965 |
| GO:0021915 | neural tube development | 0.000568641857073429 |
| GO:0016331 | morphogenesis of embryonic epithelium | 0.000636282393872113 |
| GO:0003677 | DNA binding | 0.000636282393872113 |
| GO:0007399 | nervous system development | 0.000835223444455235 |
| GO:0002009 | morphogenesis of an epithelium | 0.00136167516678533 |
| GO:0035239 | tube morphogenesis | 0.00181898416272182 |
| GO:0003676 | nucleic acid binding | 0.00213504303258981 |
| GO:0007420 | brain development | 0.00243345122482529 |
| GO:0048598 | embryonic morphogenesis | 0.00256023272294392 |
| GO:0035295 | tube development | 0.00256023272294392 |
| GO:0016337 | cell-cell adhesion | 0.0025884509832289 |
| GO:0043009 | chordate embryonic development | 0.00269954463698739 |
| GO:0009792 | embryonic development ending in birth or egg hatching | 0.00269954463698739 |
| GO:0005634 | nucleus | 0.00625387709903602 |
| GO:0008589 | regulation of smoothened signaling pathway | 0.00703697243384536 |
| GO:0048731 | system development | 0.00703697243384536 |
| GO:0048869 | cellular developmental process | 0.00703697243384536 |
| GO:0030154 | cell differentiation | 0.00703697243384536 |
| GO:0009790 | embryonic development | 0.00815239420749265 |
| GO:0008270 | zinc ion binding | 0.0084646283988294 |
| GO:0048856 | anatomical structure development | 0.00910520032603384 |
| GO:0007275 | multicellular organismal development | 0.0116707777989934 |
| GO:0022610 | biological adhesion | 0.0116707777989934 |
| GO:0007155 | cell adhesion | 0.0116707777989934 |
| GO:0007224 | smoothened signaling pathway | 0.0116707777989934 |
| GO:0048066 | pigmentation during development | 0.0117203371206961 |
| GO:0046914 | transition metal ion binding | 0.0125989430938281 |
| GO:0032502 | developmental process | 0.0221024338513604 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0221024338513604 |
| GO:0043227 | membrane-bound organelle | 0.0221024338513604 |
| GO:0043169 | cation binding | 0.0288932550287507 |
| GO:0009653 | anatomical structure morphogenesis | 0.0318776641924248 |
| GO:0030900 | forebrain development | 0.0319765146532927 |
| GO:0043229 | intracellular organelle | 0.0319765146532927 |
| GO:0043226 | organelle | 0.0319765146532927 |
| GO:0046872 | metal ion binding | 0.0322470960645324 |
| GO:0043167 | ion binding | 0.0334005799442731 |
| GO:0048513 | organ development | 0.0386898252973023 |
| GO:0032501 | multicellular organismal process | 0.045169113728162 |
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 |
|---|---|---|
| CNS neuron (sensu Vertebrata) | 6.87e-13 | 23 |
| neuroblast (sensu Vertebrata) | 6.87e-13 | 23 |
| neural cell | 5.12e-11 | 43 |
| ectodermal cell | 1.38e-10 | 44 |
| neurectodermal cell | 1.38e-10 | 44 |
| non-terminally differentiated cell | 1.02e-08 | 49 |
| neuron | 4.62e-08 | 33 |
| neuronal stem cell | 4.62e-08 | 33 |
| neuroblast | 4.62e-08 | 33 |
| electrically signaling cell | 4.62e-08 | 33 |
| Ontology term | p-value | n |
|---|---|---|
| neurectoderm | 9.21e-20 | 64 |
| neural plate | 9.21e-20 | 64 |
| presumptive neural plate | 9.21e-20 | 64 |
| central nervous system | 1.74e-19 | 73 |
| nervous system | 1.39e-18 | 75 |
| regional part of nervous system | 1.70e-18 | 54 |
| neural tube | 6.46e-18 | 52 |
| neural rod | 6.46e-18 | 52 |
| future spinal cord | 6.46e-18 | 52 |
| neural keel | 6.46e-18 | 52 |
| ectoderm-derived structure | 8.68e-18 | 95 |
| ectoderm | 8.68e-18 | 95 |
| presumptive ectoderm | 8.68e-18 | 95 |
| ecto-epithelium | 1.56e-16 | 73 |
| regional part of brain | 5.02e-13 | 46 |
| pre-chordal neural plate | 1.09e-12 | 49 |
| brain | 1.48e-12 | 47 |
| future brain | 1.48e-12 | 47 |
| posterior neural tube | 1.09e-10 | 12 |
| chordal neural plate | 1.09e-10 | 12 |
| structure with developmental contribution from neural crest | 1.82e-10 | 92 |
| anterior neural tube | 1.27e-09 | 40 |
| regional part of forebrain | 3.11e-09 | 39 |
| forebrain | 3.11e-09 | 39 |
| future forebrain | 3.11e-09 | 39 |
| gray matter | 2.05e-08 | 34 |
| spinal cord | 4.56e-07 | 6 |
| dorsal region element | 4.56e-07 | 6 |
| dorsum | 4.56e-07 | 6 |
| regional part of spinal cord | 9.34e-07 | 5 |
| gray matter of spinal cord | 9.34e-07 | 5 |
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 | 0.261277 |
| MA0004.1 | 0.330313 |
| MA0006.1 | 0.186435 |
| MA0007.1 | 0.316976 |
| MA0009.1 | 0.743257 |
| MA0014.1 | 0.144697 |
| MA0017.1 | 0.598706 |
| MA0019.1 | 0.567591 |
| MA0024.1 | 1.6716 |
| MA0025.1 | 0.971686 |
| MA0027.1 | 2.37948 |
| MA0028.1 | 0.194782 |
| MA0029.1 | 0.679737 |
| MA0030.1 | 0.686088 |
| MA0031.1 | 0.651724 |
| MA0038.1 | 0.462726 |
| MA0040.1 | 0.755433 |
| MA0041.1 | 0.263922 |
| MA0042.1 | 0.252679 |
| MA0043.1 | 0.837621 |
| MA0046.1 | 0.778239 |
| MA0048.1 | 0.440822 |
| MA0050.1 | 0.365212 |
| MA0051.1 | 0.471092 |
| MA0052.1 | 0.76328 |
| MA0055.1 | 2.71747 |
| MA0056.1 | 0 |
| MA0057.1 | 2.63634 |
| MA0058.1 | 0.246908 |
| MA0059.1 | 0.714494 |
| MA0060.1 | 0.395347 |
| MA0061.1 | 0.884293 |
| MA0063.1 | 0 |
| MA0066.1 | 0.452472 |
| MA0067.1 | 1.08124 |
| MA0068.1 | 0.187364 |
| MA0069.1 | 0.76361 |
| MA0070.1 | 0.75417 |
| MA0071.1 | 0.364454 |
| MA0072.1 | 0.745922 |
| MA0073.1 | 8.00317 |
| MA0074.1 | 0.419185 |
| MA0076.1 | 0.223625 |
| MA0077.1 | 0.724865 |
| MA0078.1 | 0.502121 |
| MA0081.1 | 1.39097 |
| MA0083.1 | 0.836845 |
| MA0084.1 | 1.4063 |
| MA0087.1 | 0.794721 |
| MA0088.1 | 0.28966 |
| MA0089.1 | 0 |
| MA0090.1 | 0.299987 |
| MA0091.1 | 0.342071 |
| MA0092.1 | 0.300264 |
| MA0093.1 | 0.20148 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.408523 |
| MA0101.1 | 0.265031 |
| MA0103.1 | 0.216742 |
| MA0105.1 | 1.95127 |
| MA0106.1 | 1.26962 |
| MA0107.1 | 0.607721 |
| MA0108.2 | 0.589413 |
| MA0109.1 | 0 |
| MA0111.1 | 0.312463 |
| MA0113.1 | 0.482899 |
| MA0114.1 | 0.446898 |
| MA0115.1 | 0.84036 |
| MA0116.1 | 0.546914 |
| MA0117.1 | 0.808813 |
| MA0119.1 | 0.265536 |
| MA0122.1 | 0.828211 |
| MA0124.1 | 1.02871 |
| MA0125.1 | 0.955734 |
| MA0130.1 | 0 |
| MA0131.1 | 0.563262 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.873285 |
| MA0136.1 | 0.437601 |
| MA0139.1 | 0.103495 |
| MA0140.1 | 0.408417 |
| MA0141.1 | 0.233109 |
| MA0142.1 | 0.63775 |
| MA0143.1 | 0.49828 |
| MA0144.1 | 0.147954 |
| MA0145.1 | 0.57264 |
| MA0146.1 | 1.40012 |
| MA0147.1 | 0.157258 |
| MA0148.1 | 0.344843 |
| MA0149.1 | 0.269772 |
| MA0062.2 | 0.0791588 |
| MA0035.2 | 0.412747 |
| MA0039.2 | 0.0387728 |
| MA0138.2 | 0.555696 |
| MA0002.2 | 0.343346 |
| MA0137.2 | 0.230686 |
| MA0104.2 | 0.11535 |
| MA0047.2 | 0.46201 |
| MA0112.2 | 0.57262 |
| MA0065.2 | 0.314773 |
| MA0150.1 | 0.316876 |
| MA0151.1 | 0 |
| MA0152.1 | 0.46211 |
| MA0153.1 | 0.889592 |
| MA0154.1 | 1.16232 |
| MA0155.1 | 0.637282 |
| MA0156.1 | 0.222905 |
| MA0157.1 | 0.606944 |
| MA0158.1 | 0 |
| MA0159.1 | 0.165031 |
| MA0160.1 | 0.347545 |
| MA0161.1 | 0 |
| MA0162.1 | 1.19805 |
| MA0163.1 | 0.355774 |
| MA0164.1 | 0.437937 |
| MA0080.2 | 0.212408 |
| MA0018.2 | 0.446948 |
| MA0099.2 | 0.549696 |
| MA0079.2 | 1.59098 |
| MA0102.2 | 1.45844 |
| MA0258.1 | 0.135621 |
| MA0259.1 | 0.14914 |
| MA0442.1 | 0 |
