MCL coexpression mm9:1355: Difference between revisions
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{{MCL_coexpression_mm9 | 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|coexpression_dpi_cluster_scores_median=0.0662288257551475,-0.0475000168233615,0.0553643120926897,-0.0515243514834304,-0.0347220195790693,-0.0115336617218672,-0.115959495504421,-0.163555110260221,-0.163555110260221,-0.117886175997944,-0.168186332803575,-0.185839133364619,-0.163555110260221,-0.145356371725211,-0.180012129001625,-0.152280894825693,-0.170942070775897,-0.170701349370936,-0.202505196047913,-0.162095299887891,0.0393484186921031,-0.146495150941107,-0.202505196047913,-0.103270637655707,-0.121494357172567,-0.0778681927000908,-0.0442859074854201,-0.085744024153876,-0.126949687730516,-0.104890415870761,-0.0687045778360499,-0.0265866980987024,-0.0188023063263769,-0.202505196047913,-0.0883309638267149,-0.169185470705389,-0.0480300908865189,-0.202505196047913,-0.202505196047913,-0.202505196047913,-0.162727435107865,-0.202505196047913,-0.202505196047913,0.0290340747312956,-0.00222789392793255,0.117234870439895,0.179219627174316,0.155551519470562,0.157188356349733,0.0850512555441145,0.0466188009396526,0.0303149315528513,-0.168824194940938,-0.202505196047913,-0.163555110260221,-0.0343121419033993,0.112884780398246,-0.0218999419273646,0.406215376840303,0.355398583304325,0.561527517789532,0.06374827581996,-0.0369407092486899,-0.0413931134622078,-0.179587973233171,-0.202505196047913,0.00193256872869616,0.111277523038531,0.324280455493973,0.431162030167149,0.341582457007526,0.299076207624317,0.156790138478328,0.343167129503104,0.442418707283252,0.507228341057667,-0.0831195196567693,0.185639224404062,0.0879035408486771,0.435922317958105,0.484924195847814,0.534440025308554,0.020966169628493,0.148847221117788,0.185816209020065,0.294440011767513,0.30168941837062,0.404104891813481,0.00687353541719455,0.0598811468018826,-0.0831195196567693,-0.0831195196567693,-0.162727435107865,-0.162727435107865,-0.142719115206496,-0.123106684533332,-0.0578424132672138,0.000182022120901801,-0.00589877151565102,0.110376170182623,0.0454263076579172,0.015723027982003,-0.0831195196567693,0.979947521487698,-0.0967799567960962,-0.0338810428342402,-0.163555110260221,-0.0813222511852756,-0.162727435107865,0.0154086144574107,0.068738352512679,-0.0334821847491261,-0.0038416668653766,-0.0535920207915405,0.0180013639629961,-0.00899702318971152,0.0712925241881543,-0.0867847667639478,-0.202505196047913,0.0353471412966372,-0.0787399602555232,-0.117650012823073,-0.0831195196567693,0.145536511090831,0.173581806739417,-0.185235548098782,-0.202505196047913,-0.202505196047913,-0.202505196047913,0.179727087290215,0.0593337871297624,0.389069604561389,0.180785408733057,0.185261720052009,0.0532155276499066,0.10394638485993,0.127274861976373,-0.121558616900426,-0.0027459682648575,-0.0416475532817872,0.103431136446673,0.012239177772744,0.143847904445502,0.0968375580970401,0.154213019355244,0.114218891966671,0.144324011450157,-0.0474970433912435,0.232665594109755,0.218392557480818,0.201614767217014,0.217718986126747,0.0796567010442597,0.0276532019760352,-0.12123635051835,0.0181849524232715,-0.202505196047913,-0.192840527909458,-0.202505196047913,0.0549851902611915,0.0697363985204909,0.0740631355462575,0.132091347983904,0.111330727527388,0.0571648022481376,0.00313031473751585,-0.0159594027618102,0.100585385608405,0.0611164642996443,-0.00210435872065595,-0.0189212273128435,0.0258814451322622,-0.0789697796480142,-0.0817331382335182,0.186065437889435,0.440061374232161,-0.202505196047913,-0.111305296217523,0.0786322191219461,0.121739539812451,0.0569486898749473,-0.0413762835840479,-0.05467649093324,-0.0520590679261913,-0.0338518595507095,0.0201060282697265,-0.0490584604063425,-0.0612024662520727,-0.042013291902075,-0.193135007553099,-0.0464784510931946,-0.0569102592654731,0.0925977171969874,0.0898134063135234,-0.0831195196567693,0.0467441579074832,-0.00761688899952815,0.108501963084016,0.0656930773350863,-0.0424619567336002,-0.0546503387838495,-0.0741721965277782,-0.163555110260221,-0.0311108010369844,-0.170451133007366,-0.16180238530282,-0.128555746626062,-0.110879859310202,-0.114297994257225,-0.0679905840994321,-0.108888518462591,-0.0666923097823186,-0.0834244867510489,-0.099128914954621,-0.0981919106461228,-0.0773345623421798,-0.0641726336970268,-0.111062384574117,-0.0382919714894958,0.164524752097908,0.114124027501987,0.0237196516869558,-0.0169546616910224,0.0941149776967,0.0926008655670286,0.113661908286755,0.0412206489322623,0.112781728023163,0.18995290498563,-0.0119865267147236,0.0288363584401834,0.000694552828306315,-0.202505196047913,-0.202505196047913,-0.162727435107865,-0.0908666464695434,0.0729971004082304,0.0912763814407744,-0.0142936680244538,-0.0649597814478272,0.00222084184475193,0.0073612857406126,0.1133222127621,0.0739273137219797,-0.0150593498901363,0.065078628824403,0.138446306113481,0.10452473891765,-0.00367697532467955,0.117077149857851,-0.0644262873017429,0.0303002943917654,0.189155117104946,0.0107373811087244,-0.0831195196567693,-0.000596063677191949,0.025101232661179,0.0280118228961837,0.0220390008600978,-0.0056494494643118,0.0890812291321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| |||
|gostat_on_MCL_coexpression=GO:0046935;1-phosphatidylinositol-3-kinase regulator activity;0.0246534816194598;18710!GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0308033469676536;18710,12927!GO:0048008;platelet-derived growth factor receptor signaling pathway;0.0308033469676536;12927!GO:0035014;phosphoinositide 3-kinase regulator activity;0.0308033469676536;18710!GO:0007167;enzyme linked receptor protein signaling pathway;0.0351845416805496;18710,12927!GO:0005942;phosphoinositide 3-kinase complex;0.0351845416805496;18710!GO:0016339;calcium-dependent cell-cell adhesion;0.0351845416805496;93706!GO:0030054;cell junction;0.0473742144187332;12927,93706! | |||
|ontology_enrichment_celltype=CL:0002319!5.92e-13!43;CL:0000221!5.97e-13!44;CL:0000133!5.97e-13!44;CL:0000055!1.55e-12!49;CL:0000117!4.22e-12!23;CL:0000337!4.22e-12!23;CL:0000540!1.10e-11!33;CL:0000047!1.10e-11!33;CL:0000031!1.10e-11!33;CL:0000404!1.10e-11!33;CL:0000393!4.23e-11!39;CL:0000211!4.23e-11!39 | |||
|ontology_enrichment_disease= | |||
|ontology_enrichment_uberon=UBERON:0001017!5.92e-26!73;UBERON:0001016!7.83e-26!75;UBERON:0004121!1.42e-24!95;UBERON:0000924!1.42e-24!95;UBERON:0006601!1.42e-24!95;UBERON:0002346!5.70e-24!64;UBERON:0003075!5.70e-24!64;UBERON:0007284!5.70e-24!64;UBERON:0001049!2.53e-23!52;UBERON:0005068!2.53e-23!52;UBERON:0006241!2.53e-23!52;UBERON:0007135!2.53e-23!52;UBERON:0000073!6.14e-23!54;UBERON:0010371!2.15e-21!73;UBERON:0010314!2.33e-21!92;UBERON:0000955!2.81e-20!47;UBERON:0006238!2.81e-20!47;UBERON:0002616!6.47e-20!46;UBERON:0002020!1.36e-18!34;UBERON:0003056!2.25e-18!49;UBERON:0003080!1.06e-17!40;UBERON:0002780!3.47e-17!39;UBERON:0001890!3.47e-17!39;UBERON:0006240!3.47e-17!39;UBERON:0003528!1.31e-15!29;UBERON:0002791!1.31e-15!29;UBERON:0001893!1.31e-15!29;UBERON:0000956!2.17e-12!21;UBERON:0001869!2.17e-12!21;UBERON:0000203!2.17e-12!21;UBERON:0000025!8.09e-11!114;UBERON:0004111!3.01e-10!122;UBERON:0002619!5.06e-10!17;UBERON:0000468!7.65e-08!333 | |||
}} | |||
Latest revision as of 16:48, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr14:121434731..121434742,+ | p7@Farp1 |
| Mm9::chr18:37966664..37966677,+ | p@chr18:37966664..37966677 + |
| Mm9::chr1:95532218..95532229,- | p4@Stk25 |
| Mm9::chr4:115894226..115894237,+ | p3@Pik3r3 |
| Mm9::chr8:114267768..114267787,- | p3@Bcar1 |
| Mm9::chr8:127187311..127187332,- | p4@2310022B05Rik |
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:0046935 | 1-phosphatidylinositol-3-kinase regulator activity | 0.0246534816194598 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.0308033469676536 |
| GO:0048008 | platelet-derived growth factor receptor signaling pathway | 0.0308033469676536 |
| GO:0035014 | phosphoinositide 3-kinase regulator activity | 0.0308033469676536 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.0351845416805496 |
| GO:0005942 | phosphoinositide 3-kinase complex | 0.0351845416805496 |
| GO:0016339 | calcium-dependent cell-cell adhesion | 0.0351845416805496 |
| GO:0030054 | cell junction | 0.0473742144187332 |
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 |
|---|---|---|
| neural cell | 5.92e-13 | 43 |
| ectodermal cell | 5.97e-13 | 44 |
| neurectodermal cell | 5.97e-13 | 44 |
| non-terminally differentiated cell | 1.55e-12 | 49 |
| CNS neuron (sensu Vertebrata) | 4.22e-12 | 23 |
| neuroblast (sensu Vertebrata) | 4.22e-12 | 23 |
| neuron | 1.10e-11 | 33 |
| neuronal stem cell | 1.10e-11 | 33 |
| neuroblast | 1.10e-11 | 33 |
| electrically signaling cell | 1.10e-11 | 33 |
| electrically responsive cell | 4.23e-11 | 39 |
| electrically active cell | 4.23e-11 | 39 |
| Ontology term | p-value | n |
|---|---|---|
| central nervous system | 5.92e-26 | 73 |
| nervous system | 7.83e-26 | 75 |
| ectoderm-derived structure | 1.42e-24 | 95 |
| ectoderm | 1.42e-24 | 95 |
| presumptive ectoderm | 1.42e-24 | 95 |
| neurectoderm | 5.70e-24 | 64 |
| neural plate | 5.70e-24 | 64 |
| presumptive neural plate | 5.70e-24 | 64 |
| neural tube | 2.53e-23 | 52 |
| neural rod | 2.53e-23 | 52 |
| future spinal cord | 2.53e-23 | 52 |
| neural keel | 2.53e-23 | 52 |
| regional part of nervous system | 6.14e-23 | 54 |
| ecto-epithelium | 2.15e-21 | 73 |
| structure with developmental contribution from neural crest | 2.33e-21 | 92 |
| brain | 2.81e-20 | 47 |
| future brain | 2.81e-20 | 47 |
| regional part of brain | 6.47e-20 | 46 |
| gray matter | 1.36e-18 | 34 |
| pre-chordal neural plate | 2.25e-18 | 49 |
| anterior neural tube | 1.06e-17 | 40 |
| regional part of forebrain | 3.47e-17 | 39 |
| forebrain | 3.47e-17 | 39 |
| future forebrain | 3.47e-17 | 39 |
| brain grey matter | 1.31e-15 | 29 |
| regional part of telencephalon | 1.31e-15 | 29 |
| telencephalon | 1.31e-15 | 29 |
| cerebral cortex | 2.17e-12 | 21 |
| cerebral hemisphere | 2.17e-12 | 21 |
| pallium | 2.17e-12 | 21 |
| tube | 8.09e-11 | 114 |
| anatomical conduit | 3.01e-10 | 122 |
| regional part of cerebral cortex | 5.06e-10 | 17 |
| multi-cellular organism | 7.65e-08 | 333 |
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 | 1.03722 |
| MA0004.1 | 1.3269 |
| MA0006.1 | 0.359699 |
| MA0007.1 | 1.29371 |
| MA0009.1 | 0.987341 |
| MA0014.1 | 1.71935 |
| MA0017.1 | 0.387481 |
| MA0019.1 | 0.800946 |
| MA0024.1 | 0.942716 |
| MA0025.1 | 1.22395 |
| MA0027.1 | 2.64231 |
| MA0028.1 | 0.370592 |
| MA0029.1 | 0.920529 |
| MA0030.1 | 0.927235 |
| MA0031.1 | 0.890871 |
| MA0038.1 | 0.686534 |
| MA0040.1 | 1.00009 |
| MA0041.1 | 0.457338 |
| MA0042.1 | 0.443591 |
| MA0043.1 | 1.08567 |
| MA0046.1 | 1.02391 |
| MA0048.1 | 0.486223 |
| MA0050.1 | 0.57678 |
| MA0051.1 | 0.695779 |
| MA0052.1 | 1.00829 |
| MA0055.1 | 0.212634 |
| MA0056.1 | 0 |
| MA0057.1 | 1.43735 |
| MA0058.1 | 1.11298 |
| MA0059.1 | 1.14076 |
| MA0060.1 | 0.275911 |
| MA0061.1 | 0.307097 |
| MA0063.1 | 0 |
| MA0066.1 | 1.61836 |
| MA0067.1 | 1.33603 |
| MA0068.1 | 0.153907 |
| MA0069.1 | 1.00864 |
| MA0070.1 | 0.998765 |
| MA0071.1 | 0.575909 |
| MA0072.1 | 0.990133 |
| MA0073.1 | 0.270597 |
| MA0074.1 | 0.638014 |
| MA0076.1 | 0.407465 |
| MA0077.1 | 0.968053 |
| MA0078.1 | 0.729877 |
| MA0081.1 | 0.473489 |
| MA0083.1 | 1.08487 |
| MA0084.1 | 1.66561 |
| MA0087.1 | 1.04109 |
| MA0088.1 | 1.19273 |
| MA0089.1 | 0 |
| MA0090.1 | 0.500693 |
| MA0091.1 | 0.55008 |
| MA0092.1 | 0.501022 |
| MA0093.1 | 0.988233 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.626021 |
| MA0101.1 | 0.458688 |
| MA0103.1 | 0.398766 |
| MA0105.1 | 0.199622 |
| MA0106.1 | 0.737893 |
| MA0107.1 | 0.392331 |
| MA0108.2 | 0.824407 |
| MA0109.1 | 0 |
| MA0111.1 | 0.515457 |
| MA0113.1 | 0.708789 |
| MA0114.1 | 0.304661 |
| MA0115.1 | 1.08851 |
| MA0116.1 | 0.359483 |
| MA0117.1 | 1.05576 |
| MA0119.1 | 0.459301 |
| MA0122.1 | 1.07591 |
| MA0124.1 | 1.28237 |
| MA0125.1 | 1.20757 |
| MA0130.1 | 0 |
| MA0131.1 | 0.796279 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.1226 |
| MA0136.1 | 0.658622 |
| MA0139.1 | 0.243463 |
| MA0140.1 | 0.625902 |
| MA0141.1 | 0.419361 |
| MA0142.1 | 0.876028 |
| MA0143.1 | 0.725672 |
| MA0144.1 | 0.307873 |
| MA0145.1 | 1.24552 |
| MA0146.1 | 0.990842 |
| MA0147.1 | 0.858298 |
| MA0148.1 | 0.553294 |
| MA0149.1 | 0.464445 |
| MA0062.2 | 0.204999 |
| MA0035.2 | 0.630778 |
| MA0039.2 | 1.76222 |
| MA0138.2 | 0.788113 |
| MA0002.2 | 0.689262 |
| MA0137.2 | 0.416331 |
| MA0104.2 | 1.33199 |
| MA0047.2 | 0.685741 |
| MA0112.2 | 0.37938 |
| MA0065.2 | 0.119561 |
| MA0150.1 | 0.520653 |
| MA0151.1 | 0 |
| MA0152.1 | 0.685852 |
| MA0153.1 | 1.13945 |
| MA0154.1 | 0.480757 |
| MA0155.1 | 1.33283 |
| MA0156.1 | 0.406559 |
| MA0157.1 | 0.843181 |
| MA0158.1 | 0 |
| MA0159.1 | 0.331229 |
| MA0160.1 | 0.556423 |
| MA0161.1 | 0 |
| MA0162.1 | 1.53386 |
| MA0163.1 | 1.4645 |
| MA0164.1 | 0.658997 |
| MA0080.2 | 0.393257 |
| MA0018.2 | 0.669032 |
| MA0099.2 | 0.781628 |
| MA0079.2 | 1.5775 |
| MA0102.2 | 1.7182 |
| MA0258.1 | 0.290587 |
| MA0259.1 | 1.5079 |
| MA0442.1 | 0 |
