MCL coexpression mm9:480: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| Line 6: | Line 6: | ||
|ontology_enrichment_disease= | |ontology_enrichment_disease= | ||
|ontology_enrichment_uberon=UBERON:0002384!6.75e-09!46;UBERON:0003350!8.53e-08!9;UBERON:0004808!8.53e-08!9;UBERON:0001277!8.53e-08!9;UBERON:0000485!3.24e-07!11;UBERON:0000490!5.19e-07!66 | |ontology_enrichment_uberon=UBERON:0002384!6.75e-09!46;UBERON:0003350!8.53e-08!9;UBERON:0004808!8.53e-08!9;UBERON:0001277!8.53e-08!9;UBERON:0000485!3.24e-07!11;UBERON:0000490!5.19e-07!66 | ||
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.59339,1.04664,0.238864,0.110365,0.250289,0.867472,0.057666,0.223561,1.12301,0.288187,0.314655,0.210446,0.890651,0.383709,0,1.26156,0.105493,0.1896,0.212558,0.160516,0.138504,0.334384,0.109412,0.561942,0.942903,0.0471703,0.736859,0.431865,0.547046,0.710801,0.598971,0.104128,0.352983,0.384512,0.972588,1.1076,0.311629,0.290566,0.902111,0.107883,0.720345,0.0429639,0.387037,0.409286,0.651235,0.433813,0.279902,0.0308934,0.436869,0.48979,0.994193,0.521833,1.73733,0.749094,0.341233,0.147717,0.820802,0.378703,0.339495,0.580338,1.01224,0.240695,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.991414,0.218482,1.47747,0.781142,1.92288,0.951256,0.153229,0.423705,0.564426,0.163487,0.479273,0.521544,0.388944,0.443997,1.6106,1.66325,0.016756,0.125355,1.95441,1.38183,0.947651,0.676142,0.610915,0.114049,0.595467,0.0741053,0.0565042,0.613539,0.43404,0.469526,0.325002,0.59871,0.715894,0.490329,0.489372,0.259558,0.543989,0.276621,0.965679,0.487082,0.201092,0.717588,0.493275,1.44634,0.954503,0.346836,1.27671,0.678491,0.506861,0.31898,0.786314,0.46068,0.946372,0.422901,1.00724,1.39345,0.331666,0.60459,0.8786,0.115924,0.699779,1.22651,0.850049,0.352905,0.975524,0.00977832,0.212784,0.722951,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.726856,1.71556,0.963294,0.733963,0.56364,0.352111,0.81211,0.382849,0.128633,0.204546,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.663991,0.313326,1.14539 | |||
}} | }} | ||
Revision as of 18:25, 26 November 2012
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr10:41238883..41238909,- | p@chr10:41238883..41238909 - |
| Mm9::chr10:77069406..77069425,+ | p8@Sumo3 |
| Mm9::chr10:79623652..79623666,- | p@chr10:79623652..79623666 - |
| Mm9::chr11:117515863..117515866,- | p@chr11:117515863..117515866 - |
| Mm9::chr12:111829796..111829818,- | p@chr12:111829796..111829818 - |
| Mm9::chr13:93380879..93380905,- | p@chr13:93380879..93380905 - |
| Mm9::chr15:96116436..96116455,+ | p@chr15:96116436..96116455 + |
| Mm9::chr18:31794423..31794465,- | p@chr18:31794423..31794465 - |
| Mm9::chr19:53674495..53674503,- | p@chr19:53674495..53674503 - |
| Mm9::chr19:7292351..7292358,+ | p@chr19:7292351..7292358 + |
| Mm9::chr3:146184120..146184147,+ | p@chr3:146184120..146184147 + |
| Mm9::chr5:112705376..112705388,- | p@chr5:112705376..112705388 - |
| Mm9::chr5:139853670..139853699,+ | p1@D830046C22Rik p3@Gpr146 |
| Mm9::chr6:85401482..85401496,+ | p4@Cct7 |
| Mm9::chr8:32260438..32260442,- | p1@ENSMUST00000157627 |
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:0019949 | SUMO conjugating enzyme activity | 0.00945807736893712 |
| GO:0016925 | protein sumoylation | 0.00945807736893712 |
| GO:0005832 | chaperonin-containing T-complex | 0.00945807736893712 |
| GO:0032446 | protein modification by small protein conjugation | 0.0455539663794155 |
| GO:0051082 | unfolded protein binding | 0.0469544530664094 |
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 |
|---|---|---|
| hematopoietic cell | 1.86e-13 | 32 |
| hematopoietic oligopotent progenitor cell | 1.86e-13 | 32 |
| hematopoietic stem cell | 1.86e-13 | 32 |
| angioblastic mesenchymal cell | 1.86e-13 | 32 |
| hematopoietic multipotent progenitor cell | 1.86e-13 | 32 |
| nucleate cell | 2.95e-11 | 16 |
| hematopoietic lineage restricted progenitor cell | 2.00e-10 | 25 |
| lymphoid lineage restricted progenitor cell | 1.11e-09 | 12 |
| T cell | 6.14e-09 | 11 |
| pro-T cell | 6.14e-09 | 11 |
| connective tissue cell | 6.75e-09 | 46 |
| mesenchymal cell | 6.75e-09 | 46 |
| lymphocyte | 8.27e-09 | 13 |
| common lymphoid progenitor | 8.27e-09 | 13 |
| somatic cell | 3.56e-08 | 118 |
| mature alpha-beta T cell | 8.38e-08 | 9 |
| alpha-beta T cell | 8.38e-08 | 9 |
| immature T cell | 8.38e-08 | 9 |
| mature T cell | 8.38e-08 | 9 |
| immature alpha-beta T cell | 8.38e-08 | 9 |
| intestinal epithelial cell | 8.53e-08 | 9 |
| epithelial cell of alimentary canal | 8.53e-08 | 9 |
| stem cell | 2.02e-07 | 97 |
| motile cell | 2.52e-07 | 54 |
| CD4-positive, alpha-beta T cell | 4.34e-07 | 8 |
| animal cell | 5.48e-07 | 115 |
| eukaryotic cell | 5.48e-07 | 115 |
| leukocyte | 6.09e-07 | 17 |
| nongranular leukocyte | 6.09e-07 | 17 |
| Ontology term | p-value | n |
|---|---|---|
| connective tissue | 6.75e-09 | 46 |
| epithelium of mucosa | 8.53e-08 | 9 |
| gastrointestinal system epithelium | 8.53e-08 | 9 |
| intestinal epithelium | 8.53e-08 | 9 |
| simple columnar epithelium | 3.24e-07 | 11 |
| unilaminar epithelium | 5.19e-07 | 66 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
