MCL coexpression mm9:301: Difference between revisions
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{{MCL_coexpression_mm9 | 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biogenesis and assembly;5.11680186249144e-07;52513,66254,69663,59014,53414!GO:0022613;ribonucleoprotein complex biogenesis and assembly;3.20675718272105e-06;52513,66254,69663,59014,53414!GO:0005730;nucleolus;4.9783549932582e-06;52513,18432,64424,74111!GO:0016072;rRNA metabolic process;9.72423441477556e-06;52513,66254,69663!GO:0006364;rRNA processing;9.72423441477556e-06;52513,66254,69663!GO:0005634;nucleus;1.35386557805915e-05;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0003723;RNA binding;2.30020001477502e-05;52513,22185,226169,66254,69663,74111!GO:0006396;RNA processing;2.86814449429933e-05;52513,22185,68626,66254,69663!GO:0016070;RNA metabolic process;0.00418132620189929;66254,52513,22185,68626,226169,18432,69663,64424!GO:0043231;intracellular membrane-bound organelle;0.00418132620189929;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0043227;membrane-bound organelle;0.00418132620189929;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0057915285466571;66254,51797,52513,22185,68626,226169,18432,69663,64424!GO:0044428;nuclear part;0.0057915285466571;52513,22185,18432,64424,74111!GO:0031981;nuclear lumen;0.00651548456133426;52513,18432,64424,74111!GO:0006996;organelle organization and biogenesis;0.00855697563088129;52513,66254,69663,59014,53414!GO:0031974;membrane-enclosed lumen;0.00855697563088129;52513,18432,64424,74111!GO:0043233;organelle lumen;0.00855697563088129;52513,18432,64424,74111!GO:0010467;gene expression;0.00855697563088129;66254,52513,22185,68626,226169,18432,69663,64424!GO:0031074;nucleocytoplasmic shuttling complex;0.00855697563088129;18432!GO:0042564;NLS-dependent protein nuclear import complex;0.00855697563088129;18432!GO:0001651;dense fibrillar component;0.00855697563088129;!GO:0003676;nucleic acid binding;0.00929918789864357;66254,74111,52513,22185,226169,18432,69663,64424!GO:0043229;intracellular organelle;0.0121978450728034;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0043226;organelle;0.0121978450728034;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0003883;CTP synthase activity;0.0138156121431303;51797!GO:0030515;snoRNA binding;0.0138156121431303;!GO:0000179;rRNA (adenine-N6,N6-)-dimethyltransferase activity;0.0179509488968946;66254!GO:0016433;rRNA (adenine) methyltransferase activity;0.0179509488968946;66254!GO:0008649;rRNA methyltransferase activity;0.0179509488968946;66254!GO:0008026;ATP-dependent helicase activity;0.0181160658139124;52513,69663!GO:0000154;rRNA modification;0.0224270101912869;66254!GO:0009303;rRNA transcription;0.0271701114396692;64424!GO:0016779;nucleotidyltransferase activity;0.0285973935560174;18432,64424!GO:0004386;helicase activity;0.0388005106397328;52513,69663!GO:0016043;cellular component organization and 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| |||
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}} | |||
Latest revision as of 15:03, 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:0042254 | ribosome biogenesis and assembly | 5.11680186249144e-07 |
| GO:0022613 | ribonucleoprotein complex biogenesis and assembly | 3.20675718272105e-06 |
| GO:0005730 | nucleolus | 4.9783549932582e-06 |
| GO:0016072 | rRNA metabolic process | 9.72423441477556e-06 |
| GO:0006364 | rRNA processing | 9.72423441477556e-06 |
| GO:0005634 | nucleus | 1.35386557805915e-05 |
| GO:0003723 | RNA binding | 2.30020001477502e-05 |
| GO:0006396 | RNA processing | 2.86814449429933e-05 |
| GO:0016070 | RNA metabolic process | 0.00418132620189929 |
| GO:0043231 | intracellular membrane-bound organelle | 0.00418132620189929 |
| GO:0043227 | membrane-bound organelle | 0.00418132620189929 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0057915285466571 |
| GO:0044428 | nuclear part | 0.0057915285466571 |
| GO:0031981 | nuclear lumen | 0.00651548456133426 |
| GO:0006996 | organelle organization and biogenesis | 0.00855697563088129 |
| GO:0031974 | membrane-enclosed lumen | 0.00855697563088129 |
| GO:0043233 | organelle lumen | 0.00855697563088129 |
| GO:0010467 | gene expression | 0.00855697563088129 |
| GO:0031074 | nucleocytoplasmic shuttling complex | 0.00855697563088129 |
| GO:0042564 | NLS-dependent protein nuclear import complex | 0.00855697563088129 |
| GO:0001651 | dense fibrillar component | 0.00855697563088129 |
| GO:0003676 | nucleic acid binding | 0.00929918789864357 |
| GO:0043229 | intracellular organelle | 0.0121978450728034 |
| GO:0043226 | organelle | 0.0121978450728034 |
| GO:0003883 | CTP synthase activity | 0.0138156121431303 |
| GO:0030515 | snoRNA binding | 0.0138156121431303 |
| GO:0000179 | rRNA (adenine-N6,N6-)-dimethyltransferase activity | 0.0179509488968946 |
| GO:0016433 | rRNA (adenine) methyltransferase activity | 0.0179509488968946 |
| GO:0008649 | rRNA methyltransferase activity | 0.0179509488968946 |
| GO:0008026 | ATP-dependent helicase activity | 0.0181160658139124 |
| GO:0000154 | rRNA modification | 0.0224270101912869 |
| GO:0009303 | rRNA transcription | 0.0271701114396692 |
| GO:0016779 | nucleotidyltransferase activity | 0.0285973935560174 |
| GO:0004386 | helicase activity | 0.0388005106397328 |
| GO:0016043 | cellular component organization and biogenesis | 0.0408817001251616 |
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><br><br>
| Ontology term | p-value | n |
|---|---|---|
| hematopoietic cell | 2.89e-10 | 32 |
| hematopoietic oligopotent progenitor cell | 2.89e-10 | 32 |
| hematopoietic stem cell | 2.89e-10 | 32 |
| angioblastic mesenchymal cell | 2.89e-10 | 32 |
| hematopoietic multipotent progenitor cell | 2.89e-10 | 32 |
| nucleate cell | 2.08e-09 | 16 |
| lymphocyte | 1.97e-07 | 13 |
| common lymphoid progenitor | 1.97e-07 | 13 |
| hematopoietic lineage restricted progenitor cell | 2.94e-07 | 25 |
| lymphoid lineage restricted progenitor cell | 7.24e-07 | 12 |
| stem cell | 9.02e-07 | 97 |
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 | 0.136408 |
| MA0004.1 | 3.68254 |
| MA0006.1 | 1.77843 |
| MA0007.1 | 0.319014 |
| MA0009.1 | 0.412602 |
| MA0014.1 | 0.377286 |
| MA0017.1 | 0.0425137 |
| MA0019.1 | 0.268299 |
| MA0024.1 | 0.37648 |
| MA0025.1 | 0.616209 |
| MA0027.1 | 1.99083 |
| MA0028.1 | 3.5596 |
| MA0029.1 | 0.358857 |
| MA0030.1 | 0.364159 |
| MA0031.1 | 0.335674 |
| MA0038.1 | 0.556221 |
| MA0040.1 | 0.423075 |
| MA0041.1 | 0.0680579 |
| MA0042.1 | 0.0625496 |
| MA0043.1 | 1.2388 |
| MA0046.1 | 0.442826 |
| MA0048.1 | 0.366277 |
| MA0050.1 | 1.86378 |
| MA0051.1 | 0.570537 |
| MA0052.1 | 0.429851 |
| MA0055.1 | 0.085769 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0953992 |
| MA0058.1 | 2.28588 |
| MA0059.1 | 1.29681 |
| MA0060.1 | 1.24013 |
| MA0061.1 | 1.04677 |
| MA0063.1 | 0 |
| MA0066.1 | 0.182901 |
| MA0067.1 | 0.717937 |
| MA0068.1 | 0.10147 |
| MA0069.1 | 0.430137 |
| MA0070.1 | 0.421986 |
| MA0071.1 | 0.393361 |
| MA0072.1 | 0.414891 |
| MA0073.1 | 0.00137944 |
| MA0074.1 | 0.937227 |
| MA0076.1 | 6.1517 |
| MA0077.1 | 0.396883 |
| MA0078.1 | 0.218627 |
| MA0081.1 | 0.551199 |
| MA0083.1 | 0.494326 |
| MA0084.1 | 1.02883 |
| MA0087.1 | 0.457205 |
| MA0088.1 | 1.38927 |
| MA0089.1 | 0 |
| MA0090.1 | 0.0869074 |
| MA0091.1 | 0.724669 |
| MA0092.1 | 0.29369 |
| MA0093.1 | 4.31452 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.465083 |
| MA0101.1 | 1.33732 |
| MA0103.1 | 0.175527 |
| MA0105.1 | 0.182808 |
| MA0106.1 | 0.224053 |
| MA0107.1 | 1.05433 |
| MA0108.2 | 0.285422 |
| MA0109.1 | 0 |
| MA0111.1 | 0.644717 |
| MA0113.1 | 1.11639 |
| MA0114.1 | 0.0900443 |
| MA0115.1 | 0.497446 |
| MA0116.1 | 0.918929 |
| MA0117.1 | 0.469566 |
| MA0119.1 | 0.0688632 |
| MA0122.1 | 0.486676 |
| MA0124.1 | 0.668899 |
| MA0125.1 | 0.601578 |
| MA0130.1 | 0 |
| MA0131.1 | 0.731896 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.526836 |
| MA0136.1 | 0.988731 |
| MA0139.1 | 0.731715 |
| MA0140.1 | 0.152839 |
| MA0141.1 | 0.197414 |
| MA0142.1 | 0.324241 |
| MA0143.1 | 0.215799 |
| MA0144.1 | 1.44299 |
| MA0145.1 | 0.207994 |
| MA0146.1 | 0.373398 |
| MA0147.1 | 5.59323 |
| MA0148.1 | 0.112635 |
| MA0149.1 | 0.0709954 |
| MA0062.2 | 8.01329 |
| MA0035.2 | 0.472078 |
| MA0039.2 | 2.23778 |
| MA0138.2 | 0.259078 |
| MA0002.2 | 0.284394 |
| MA0137.2 | 3.36204 |
| MA0104.2 | 4.03185 |
| MA0047.2 | 0.18962 |
| MA0112.2 | 1.20369 |
| MA0065.2 | 0.115736 |
| MA0150.1 | 0.318861 |
| MA0151.1 | 0 |
| MA0152.1 | 0.55517 |
| MA0153.1 | 0.541494 |
| MA0154.1 | 0.357361 |
| MA0155.1 | 0.256374 |
| MA0156.1 | 3.93316 |
| MA0157.1 | 0.299365 |
| MA0158.1 | 0 |
| MA0159.1 | 0.805512 |
| MA0160.1 | 0.739566 |
| MA0161.1 | 0 |
| MA0162.1 | 0.238334 |
| MA0163.1 | 0.203588 |
| MA0164.1 | 0.172802 |
| MA0080.2 | 0.683908 |
| MA0018.2 | 1.60801 |
| MA0099.2 | 0.254459 |
| MA0079.2 | 0.525161 |
| MA0102.2 | 1.07954 |
| MA0258.1 | 1.33284 |
| MA0259.1 | 1.45352 |
| MA0442.1 | 0 |
