MCL coexpression mm9:1664: Difference between revisions
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{{MCL_coexpression_mm9| | 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receptor cell stereocilium organization and biogenesis;0.00584378823572381;224796!GO:0002093;auditory receptor cell morphogenesis;0.00584378823572381;224796!GO:0060122;inner ear receptor stereocilium organization and biogenesis;0.00584378823572381;224796!GO:0032420;stereocilium;0.00584378823572381;224796!GO:0060119;inner ear receptor cell development;0.00584378823572381;224796!GO:0060117;auditory receptor cell development;0.00584378823572381;224796!GO:0032421;stereocilium bundle;0.00626120168113265;224796!GO:0005247;voltage-gated chloride channel activity;0.00730473529465476;224796!GO:0022844;voltage-gated anion channel activity;0.00730473529465476;224796!GO:0005902;microvillus;0.00745083000054786;224796!GO:0042491;auditory receptor cell differentiation;0.00916412246056688;224796!GO:0060113;inner ear receptor cell differentiation;0.00986139264778393;224796!GO:0050885;neuromuscular process controlling balance;0.0103309827738689;224796!GO:0042490;mechanoreceptor differentiation;0.0103309827738689;224796!GO:0050905;neuromuscular process;0.0119532032094351;224796!GO:0043168;anion binding;0.0119532032094351;224796!GO:0042472;inner ear morphogenesis;0.0119532032094351;224796!GO:0031404;chloride ion binding;0.0119532032094351;224796!GO:0005254;chloride channel activity;0.0119532032094351;224796!GO:0006821;chloride transport;0.0119532032094351;224796!GO:0042471;ear morphogenesis;0.0119532032094351;224796!GO:0005253;anion channel activity;0.0119532032094351;224796!GO:0048839;inner ear development;0.013339081842413;224796!GO:0043583;ear development;0.013878997059844;224796!GO:0007605;sensory perception of sound;0.0161288555305977;224796!GO:0050954;sensory perception of mechanical stimulus;0.0163513690057272;224796!GO:0008509;anion transmembrane transporter activity;0.0181806745111407;224796!GO:0015698;inorganic anion transport;0.0219142058839643;224796!GO:0006820;anion transport;0.0236107895653035;224796!GO:0022832;voltage-gated channel activity;0.0236107895653035;224796!GO:0005244;voltage-gated ion channel activity;0.0236107895653035;224796!GO:0007423;sensory organ development;0.0254752643401085;224796!GO:0048598;embryonic morphogenesis;0.0266954871677383;224796!GO:0022836;gated channel activity;0.0316275295730728;224796!GO:0032990;cell part morphogenesis;0.0316275295730728;224796!GO:0030030;cell projection organization and biogenesis;0.0316275295730728;224796!GO:0048858;cell projection morphogenesis;0.0316275295730728;224796!GO:0005216;ion channel activity;0.0389238037843747;224796!GO:0022838;substrate specific channel activity;0.0389238037843747;224796!GO:0042995;cell projection;0.0389238037843747;224796!GO:0022803;passive transmembrane transporter activity;0.0389238037843747;224796!GO:0015267;channel activity;0.0389238037843747;224796!GO:0009790;embryonic development;0.0448023764738825;224796!GO:0000902;cell morphogenesis;0.0448023764738825;224796!GO:0032989;cellular structure morphogenesis;0.0448023764738825;224796!GO:0009887;organ morphogenesis;0.0474490196965835;224796!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0005153!9.14e-08!17;UBERON:0007100!1.11e-07!18;UBERON:0000948!1.11e-07!18;UBERON:0005498!1.11e-07!18;UBERON:0004140!1.11e-07!18;UBERON:0009881!1.11e-07!18;UBERON:0004141!1.11e-07!18;UBERON:0003084!1.11e-07!18;UBERON:0007005!1.11e-07!18;UBERON:0004139!1.11e-07!18;UBERON:0004291!1.11e-07!18;UBERON:0004872!1.28e-07!33;UBERON:0002048!1.40e-07!14;UBERON:0000117!1.40e-07!14;UBERON:0000171!1.40e-07!14;UBERON:0000170!1.40e-07!14;UBERON:0005597!1.40e-07!14;UBERON:0000118!1.40e-07!14|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,1.31238,0.603273,1.04755,0.618805,1.70247,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,1.4086,0.727684,0.404661,2.28527,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,1.08876,0.454919,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,0.419293,1.91654,0.0637209,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,1.18377,1.64777,0.26467,0.734051,1.01481,1.86856,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,1.45025,1.23259,2.03319,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,2.60379,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,2.38494,0.412897,0.937248,0.89388,0.297538,1.05152,3.27368,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,1.5739,0.499439,0.491483,0.550229,1.16464,1.23956,0.674448,1.41481,1.82437,2.90094,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,5.05969,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,1.21592,2.6072,1.18223,0.343194,0.749664,1.26545,0.787153,1.11626,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104|tfbs_overrepresentation_jaspar=MA0003.1;1.36559,MA0004.1;0.603793,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;2.41343,MA0014.1;4.67725,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;1.12075,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.28842,MA0056.1;0,MA0057.1;1.06992,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.955135,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;1.55428,MA0072.1;1.06547,MA0073.1;0.65603,MA0074.1;2.83367,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;3.51516,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;2.77668,MA0106.1;0.809991,MA0107.1;1.15122,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;2.22941,MA0140.1;0.695713,MA0141.1;2.10278,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.822925,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;1.8247,MA0138.2;0.861035,MA0002.2;0.299191,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;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.245828,MA0163.1;0.497328,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;3.77735,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0}} | ||
Latest revision as of 17:18, 17 September 2013
Phase1 CAGE Peaks
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:0060088 | auditory receptor cell stereocilium organization and biogenesis | 0.00584378823572381 |
| GO:0002093 | auditory receptor cell morphogenesis | 0.00584378823572381 |
| GO:0060122 | inner ear receptor stereocilium organization and biogenesis | 0.00584378823572381 |
| GO:0032420 | stereocilium | 0.00584378823572381 |
| GO:0060119 | inner ear receptor cell development | 0.00584378823572381 |
| GO:0060117 | auditory receptor cell development | 0.00584378823572381 |
| GO:0032421 | stereocilium bundle | 0.00626120168113265 |
| GO:0005247 | voltage-gated chloride channel activity | 0.00730473529465476 |
| GO:0022844 | voltage-gated anion channel activity | 0.00730473529465476 |
| GO:0005902 | microvillus | 0.00745083000054786 |
| GO:0042491 | auditory receptor cell differentiation | 0.00916412246056688 |
| GO:0060113 | inner ear receptor cell differentiation | 0.00986139264778393 |
| GO:0050885 | neuromuscular process controlling balance | 0.0103309827738689 |
| GO:0042490 | mechanoreceptor differentiation | 0.0103309827738689 |
| GO:0050905 | neuromuscular process | 0.0119532032094351 |
| GO:0043168 | anion binding | 0.0119532032094351 |
| GO:0042472 | inner ear morphogenesis | 0.0119532032094351 |
| GO:0031404 | chloride ion binding | 0.0119532032094351 |
| GO:0005254 | chloride channel activity | 0.0119532032094351 |
| GO:0006821 | chloride transport | 0.0119532032094351 |
| GO:0042471 | ear morphogenesis | 0.0119532032094351 |
| GO:0005253 | anion channel activity | 0.0119532032094351 |
| GO:0048839 | inner ear development | 0.013339081842413 |
| GO:0043583 | ear development | 0.013878997059844 |
| GO:0007605 | sensory perception of sound | 0.0161288555305977 |
| GO:0050954 | sensory perception of mechanical stimulus | 0.0163513690057272 |
| GO:0008509 | anion transmembrane transporter activity | 0.0181806745111407 |
| GO:0015698 | inorganic anion transport | 0.0219142058839643 |
| GO:0006820 | anion transport | 0.0236107895653035 |
| GO:0022832 | voltage-gated channel activity | 0.0236107895653035 |
| GO:0005244 | voltage-gated ion channel activity | 0.0236107895653035 |
| GO:0007423 | sensory organ development | 0.0254752643401085 |
| GO:0048598 | embryonic morphogenesis | 0.0266954871677383 |
| GO:0022836 | gated channel activity | 0.0316275295730728 |
| GO:0032990 | cell part morphogenesis | 0.0316275295730728 |
| GO:0030030 | cell projection organization and biogenesis | 0.0316275295730728 |
| GO:0048858 | cell projection morphogenesis | 0.0316275295730728 |
| GO:0005216 | ion channel activity | 0.0389238037843747 |
| GO:0022838 | substrate specific channel activity | 0.0389238037843747 |
| GO:0042995 | cell projection | 0.0389238037843747 |
| GO:0022803 | passive transmembrane transporter activity | 0.0389238037843747 |
| GO:0015267 | channel activity | 0.0389238037843747 |
| GO:0009790 | embryonic development | 0.0448023764738825 |
| GO:0000902 | cell morphogenesis | 0.0448023764738825 |
| GO:0032989 | cellular structure morphogenesis | 0.0448023764738825 |
| GO:0009887 | organ morphogenesis | 0.0474490196965835 |
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><br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| epithelial bud | 9.14e-08 | 17 |
| primary circulatory organ | 1.11e-07 | 18 |
| heart | 1.11e-07 | 18 |
| primitive heart tube | 1.11e-07 | 18 |
| primary heart field | 1.11e-07 | 18 |
| anterior lateral plate mesoderm | 1.11e-07 | 18 |
| heart tube | 1.11e-07 | 18 |
| heart primordium | 1.11e-07 | 18 |
| cardiac mesoderm | 1.11e-07 | 18 |
| cardiogenic plate | 1.11e-07 | 18 |
| heart rudiment | 1.11e-07 | 18 |
| splanchnic layer of lateral plate mesoderm | 1.28e-07 | 33 |
| lung | 1.40e-07 | 14 |
| respiratory tube | 1.40e-07 | 14 |
| respiration organ | 1.40e-07 | 14 |
| pair of lungs | 1.40e-07 | 14 |
| lung primordium | 1.40e-07 | 14 |
| lung bud | 1.40e-07 | 14 |
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 | 1.36559 |
| MA0004.1 | 0.603793 |
| MA0006.1 | 1.07705 |
| MA0007.1 | 0.587678 |
| MA0009.1 | 2.41343 |
| MA0014.1 | 4.67725 |
| 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 | 1.12075 |
| MA0050.1 | 0.645342 |
| MA0051.1 | 0.767098 |
| MA0052.1 | 1.08379 |
| MA0055.1 | 0.28842 |
| MA0056.1 | 0 |
| MA0057.1 | 1.06992 |
| MA0058.1 | 0.50032 |
| MA0059.1 | 0.513699 |
| MA0060.1 | 0.330907 |
| MA0061.1 | 0.955135 |
| 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 | 1.55428 |
| MA0072.1 | 1.06547 |
| MA0073.1 | 0.65603 |
| MA0074.1 | 2.83367 |
| 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 | 3.51516 |
| 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 | 2.77668 |
| MA0106.1 | 0.809991 |
| MA0107.1 | 1.15122 |
| 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 | 2.22941 |
| MA0140.1 | 0.695713 |
| MA0141.1 | 2.10278 |
| MA0142.1 | 0.950155 |
| MA0143.1 | 0.797553 |
| MA0144.1 | 0.365053 |
| MA0145.1 | 0.157686 |
| MA0146.1 | 0.822925 |
| MA0147.1 | 0.378658 |
| MA0148.1 | 0.621195 |
| MA0149.1 | 0.529387 |
| MA0062.2 | 0.254018 |
| MA0035.2 | 0.700704 |
| MA0039.2 | 1.8247 |
| MA0138.2 | 0.861035 |
| MA0002.2 | 0.299191 |
| 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 | 0.173445 |
| MA0156.1 | 0.469089 |
| MA0157.1 | 0.91689 |
| MA0158.1 | 0 |
| MA0159.1 | 0.389847 |
| MA0160.1 | 0.624415 |
| MA0161.1 | 0 |
| MA0162.1 | 0.245828 |
| MA0163.1 | 0.497328 |
| MA0164.1 | 0.729558 |
| MA0080.2 | 0.455167 |
| MA0018.2 | 0.739807 |
| MA0099.2 | 0.854449 |
| MA0079.2 | 3.77735 |
| MA0102.2 | 1.79669 |
| MA0258.1 | 0.346619 |
| MA0259.1 | 0.366802 |
| MA0442.1 | 0 |
