MCL coexpression mm9:1702: Difference between revisions
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{{MCL_coexpression_mm9| | 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transmission;0.0035803288377154;14805!GO:0048172;regulation of short-term neuronal synaptic plasticity;0.0035803288377154;14805!GO:0019226;transmission of nerve impulse;0.0035803288377154;14805!GO:0015277;kainate selective glutamate receptor activity;0.00388966498699777;14805!GO:0007267;cell-cell signaling;0.00389749695633027;14805!GO:0022803;passive transmembrane transporter activity;0.00389749695633027;14805!GO:0015267;channel activity;0.00389749695633027;14805!GO:0030054;cell junction;0.00389749695633027;14805!GO:0008328;ionotropic glutamate receptor complex;0.00777741194068963;14805!GO:0065008;regulation of biological quality;0.00777741194068963;14805!GO:0048169;regulation of long-term neuronal synaptic plasticity;0.00777741194068963;14805!GO:0048168;regulation of neuronal synaptic plasticity;0.00808773078604848;14805!GO:0005234;extracellular-glutamate-gated ion channel activity;0.00808773078604848;14805!GO:0005243;gap junction channel activity;0.00808773078604848;!GO:0004970;ionotropic glutamate receptor activity;0.00808773078604848;14805!GO:0022829;wide pore channel activity;0.00808773078604848;!GO:0005922;connexon complex;0.00808773078604848;!GO:0022857;transmembrane transporter activity;0.00808773078604848;14805!GO:0048167;regulation of synaptic plasticity;0.00859373140231635;14805!GO:0050803;regulation of synapse structure and activity;0.00894108274739065;14805!GO:0005921;gap junction;0.00962521884196859;!GO:0001508;regulation of action potential;0.0130708738798452;!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0139862988667611;14805!GO:0008066;glutamate receptor activity;0.0139862988667611;14805!GO:0014704;intercalated disc;0.0139862988667611;!GO:0044459;plasma membrane part;0.0174841030919808;14805!GO:0005230;extracellular ligand-gated ion channel activity;0.0184633996099129;14805!GO:0043234;protein complex;0.0184633996099129;14805!GO:0043235;receptor complex;0.0192771606715988;14805!GO:0050877;neurological system process;0.0201328630300659;14805!GO:0015276;ligand-gated ion channel activity;0.0201328630300659;14805!GO:0022834;ligand-gated channel activity;0.0201328630300659;14805!GO:0003008;system process;0.0216390967647873;14805!GO:0005886;plasma membrane;0.0224257707744585;14805!GO:0032991;macromolecular complex;0.0226559776580504;14805!GO:0045211;postsynaptic membrane;0.0226559776580504;14805!GO:0007601;visual perception;0.0226559776580504;!GO:0050953;sensory perception of light stimulus;0.0226559776580504;!GO:0044456;synapse part;0.024057186837918;14805!GO:0005911;intercellular junction;0.0290542086819516;!GO:0042802;identical protein binding;0.0324832506934418;14805!GO:0005261;cation channel activity;0.0445290510818903;14805!GO:0022836;gated channel activity;0.0465269977220717;14805!GO:0046873;metal ion transmembrane transporter activity;0.0496500648514648;14805!|ontology_enrichment_celltype=CL:0000540!1.42e-16!33;CL:0000047!1.42e-16!33;CL:0000031!1.42e-16!33;CL:0000404!1.42e-16!33;CL:0000393!5.97e-12!39;CL:0000211!5.97e-12!39;CL:0000221!3.27e-11!44;CL:0000133!3.27e-11!44;CL:0002319!6.99e-11!43;CL:0000117!3.36e-10!23;CL:0000337!3.36e-10!23;CL:0000055!4.85e-08!49;CL:0000107!1.84e-07!9|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!6.30e-25!73;UBERON:0001016!3.14e-24!75;UBERON:0002346!3.76e-24!64;UBERON:0003075!3.76e-24!64;UBERON:0007284!3.76e-24!64;UBERON:0004121!2.92e-23!95;UBERON:0000924!2.92e-23!95;UBERON:0006601!2.92e-23!95;UBERON:0010371!3.36e-20!73;UBERON:0000073!3.82e-18!54;UBERON:0001049!3.35e-17!52;UBERON:0005068!3.35e-17!52;UBERON:0006241!3.35e-17!52;UBERON:0007135!3.35e-17!52;UBERON:0003056!1.41e-16!49;UBERON:0002020!1.49e-16!34;UBERON:0000955!1.61e-13!47;UBERON:0006238!1.61e-13!47;UBERON:0010314!1.67e-13!92;UBERON:0002616!6.42e-13!46;UBERON:0003528!1.50e-12!29;UBERON:0002791!1.50e-12!29;UBERON:0001893!1.50e-12!29;UBERON:0003080!1.99e-12!40;UBERON:0002780!7.71e-12!39;UBERON:0001890!7.71e-12!39;UBERON:0006240!7.71e-12!39;UBERON:0002021!1.22e-08!10;UBERON:0000411!1.22e-08!10;UBERON:0001950!1.22e-08!10;UBERON:0000956!3.50e-08!21;UBERON:0001869!3.50e-08!21;UBERON:0000203!3.50e-08!21;UBERON:0002410!1.84e-07!9;UBERON:0002619!3.60e-07!17|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,1.60538,0.702872,1.47559,0.728641,1.0876,0,0.930881,0.397593,0.775038,1.0421,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,1.68786,1.7724,0.699032,0.360612,0.876199,0.401916,0.631725,0.419293,0.426986,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,1.74061,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,4.38414,1.23259,0.714607,0.245132,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,1.44773,8.42284,1.87702,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,3.46853,0.3366,1.46478,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,1.23125,0.550229,1.16464,0.495367,1.61686,1.41481,0.399936,1.11665,0.607321,0.932233,0.380707,1.23809,0.879184,1.7936,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,0.230371,5.85111,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.191104|tfbs_overrepresentation_jaspar=MA0003.1;0.211284,MA0004.1;1.46913,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.187732,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;0.593503,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.562607,MA0058.1;0.50032,MA0059.1;1.27866,MA0060.1;0.330907,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;2.09333,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;0.453686,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;1.39225,MA0093.1;1.12162,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;1.28296,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;1.07655,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;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.0604336,MA0147.1;1.75115,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.749235,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;1.52809,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.477991,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;1.35147,MA0163.1;0.855539,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;1.7149,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;1.71005,MA0442.1;0}} | ||
Latest revision as of 17:21, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr16:88290431..88290442,- | p3@Grik1 |
| Mm9::chr16:88290444..88290471,- | p1@Grik1 |
| Mm9::chr2:113839356..113839374,- | p1@Gjd2 |
| Mm9::chr5:46030532..46030550,- | p2@Fam184b |
| Mm9::chr7:48153974..48153989,- | p1@A230077H06Rik |
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:0007268 | synaptic transmission | 0.0035803288377154 |
| GO:0048172 | regulation of short-term neuronal synaptic plasticity | 0.0035803288377154 |
| GO:0019226 | transmission of nerve impulse | 0.0035803288377154 |
| GO:0015277 | kainate selective glutamate receptor activity | 0.00388966498699777 |
| GO:0007267 | cell-cell signaling | 0.00389749695633027 |
| GO:0022803 | passive transmembrane transporter activity | 0.00389749695633027 |
| GO:0015267 | channel activity | 0.00389749695633027 |
| GO:0030054 | cell junction | 0.00389749695633027 |
| GO:0008328 | ionotropic glutamate receptor complex | 0.00777741194068963 |
| GO:0065008 | regulation of biological quality | 0.00777741194068963 |
| GO:0048169 | regulation of long-term neuronal synaptic plasticity | 0.00777741194068963 |
| GO:0048168 | regulation of neuronal synaptic plasticity | 0.00808773078604848 |
| GO:0005234 | extracellular-glutamate-gated ion channel activity | 0.00808773078604848 |
| GO:0005243 | gap junction channel activity | 0.00808773078604848 |
| GO:0004970 | ionotropic glutamate receptor activity | 0.00808773078604848 |
| GO:0022829 | wide pore channel activity | 0.00808773078604848 |
| GO:0005922 | connexon complex | 0.00808773078604848 |
| GO:0022857 | transmembrane transporter activity | 0.00808773078604848 |
| GO:0048167 | regulation of synaptic plasticity | 0.00859373140231635 |
| GO:0050803 | regulation of synapse structure and activity | 0.00894108274739065 |
| GO:0005921 | gap junction | 0.00962521884196859 |
| GO:0001508 | regulation of action potential | 0.0130708738798452 |
| GO:0005231 | excitatory extracellular ligand-gated ion channel activity | 0.0139862988667611 |
| GO:0008066 | glutamate receptor activity | 0.0139862988667611 |
| GO:0014704 | intercalated disc | 0.0139862988667611 |
| GO:0044459 | plasma membrane part | 0.0174841030919808 |
| GO:0005230 | extracellular ligand-gated ion channel activity | 0.0184633996099129 |
| GO:0043234 | protein complex | 0.0184633996099129 |
| GO:0043235 | receptor complex | 0.0192771606715988 |
| GO:0050877 | neurological system process | 0.0201328630300659 |
| GO:0015276 | ligand-gated ion channel activity | 0.0201328630300659 |
| GO:0022834 | ligand-gated channel activity | 0.0201328630300659 |
| GO:0003008 | system process | 0.0216390967647873 |
| GO:0005886 | plasma membrane | 0.0224257707744585 |
| GO:0032991 | macromolecular complex | 0.0226559776580504 |
| GO:0045211 | postsynaptic membrane | 0.0226559776580504 |
| GO:0007601 | visual perception | 0.0226559776580504 |
| GO:0050953 | sensory perception of light stimulus | 0.0226559776580504 |
| GO:0044456 | synapse part | 0.024057186837918 |
| GO:0005911 | intercellular junction | 0.0290542086819516 |
| GO:0042802 | identical protein binding | 0.0324832506934418 |
| GO:0005261 | cation channel activity | 0.0445290510818903 |
| GO:0022836 | gated channel activity | 0.0465269977220717 |
| GO:0046873 | metal ion transmembrane transporter activity | 0.0496500648514648 |
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 |
|---|---|---|
| neuron | 1.42e-16 | 33 |
| neuronal stem cell | 1.42e-16 | 33 |
| neuroblast | 1.42e-16 | 33 |
| electrically signaling cell | 1.42e-16 | 33 |
| electrically responsive cell | 5.97e-12 | 39 |
| electrically active cell | 5.97e-12 | 39 |
| ectodermal cell | 3.27e-11 | 44 |
| neurectodermal cell | 3.27e-11 | 44 |
| neural cell | 6.99e-11 | 43 |
| CNS neuron (sensu Vertebrata) | 3.36e-10 | 23 |
| neuroblast (sensu Vertebrata) | 3.36e-10 | 23 |
| non-terminally differentiated cell | 4.85e-08 | 49 |
| autonomic neuron | 1.84e-07 | 9 |
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 | 1.46913 |
| MA0006.1 | 1.07705 |
| MA0007.1 | 0.587678 |
| MA0009.1 | 1.06266 |
| MA0014.1 | 0.187732 |
| 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 | 0.593503 |
| MA0050.1 | 0.645342 |
| MA0051.1 | 0.767098 |
| MA0052.1 | 1.08379 |
| MA0055.1 | 0.0851423 |
| MA0056.1 | 0 |
| MA0057.1 | 0.562607 |
| MA0058.1 | 0.50032 |
| MA0059.1 | 1.27866 |
| MA0060.1 | 0.330907 |
| 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 | 2.09333 |
| 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 | 0.453686 |
| MA0089.1 | 0 |
| MA0090.1 | 0.566938 |
| MA0091.1 | 0.617887 |
| MA0092.1 | 1.39225 |
| MA0093.1 | 1.12162 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.695835 |
| MA0101.1 | 0.523409 |
| MA0103.1 | 0.460936 |
| MA0105.1 | 1.28296 |
| 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 | 1.07655 |
| 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 | 0.295945 |
| MA0140.1 | 0.695713 |
| MA0141.1 | 0.482463 |
| MA0142.1 | 0.950155 |
| MA0143.1 | 0.797553 |
| MA0144.1 | 0.365053 |
| MA0145.1 | 0.157686 |
| MA0146.1 | 0.0604336 |
| MA0147.1 | 1.75115 |
| MA0148.1 | 0.621195 |
| MA0149.1 | 0.529387 |
| MA0062.2 | 0.254018 |
| MA0035.2 | 0.700704 |
| MA0039.2 | 0.749235 |
| MA0138.2 | 0.861035 |
| MA0002.2 | 0.299191 |
| MA0137.2 | 0.479301 |
| MA0104.2 | 1.52809 |
| MA0047.2 | 0.75686 |
| MA0112.2 | 0.157681 |
| MA0065.2 | 0.477991 |
| MA0150.1 | 0.587557 |
| MA0151.1 | 0 |
| MA0152.1 | 0.756973 |
| MA0153.1 | 1.21594 |
| MA0154.1 | 0.203217 |
| MA0155.1 | 0.173445 |
| MA0156.1 | 0.469089 |
| MA0157.1 | 0.91689 |
| MA0158.1 | 0 |
| MA0159.1 | 0.389847 |
| MA0160.1 | 0.624415 |
| MA0161.1 | 0 |
| MA0162.1 | 1.35147 |
| MA0163.1 | 0.855539 |
| MA0164.1 | 0.729558 |
| MA0080.2 | 0.455167 |
| MA0018.2 | 0.739807 |
| MA0099.2 | 0.854449 |
| MA0079.2 | 1.7149 |
| MA0102.2 | 1.79669 |
| MA0258.1 | 0.346619 |
| MA0259.1 | 1.71005 |
| MA0442.1 | 0 |
