MCL coexpression mm9:3242: Difference between revisions
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.807750064546741,0.255756213076752,0.0492195847878491,0,0,0.226549106464441,0.059030951624688,0,0.105542750219401,0,0.170315527999688,0.399372339351466,0.266885070731364,0.0354470656487682,0.0411126530948397,0,0,0,0,0,0,0,0.177265236423641,0.0448571360466903,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0673620022139481,0.623163448471331,0.525389071779607,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0.690431795733084,0,0,0,0,0,0,0.00929149311320963,0,0.110319863569628,0,0,0,0,0,0,0,0.26362597042982,0,0,0.0981416444525993,0,0,0,0,0,0,0,0,0.137740408373976,0.0557366836621885,0,0,0,0,0,0,0,0.0324800223754608,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.423588899072447,0.0597835716559411,0,0,0,0,0,0,0,0,0,0,0,0.236365378443992,0.156026744954718,0.0788703512227347,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0758280215703709,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0.0635717028550276,0,0.120215008744062,0.0659019793256198,0.128841727545421,0.0586723554240733,0,0,0,0.10582914506561,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111946496400116,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0915514965999916,0.0413241580819028,0.0444296048711423,0.0816590655834685,0,0,0,0,0.111087966368681,0,0.362345599751448,0,0,0.138850957170371,0.104960908225686,0.163625352771192,0.263205259864131,0.056886356216389,0.108515345882914,0,0,0,0.0428191061329876,0,0,0,0,0,0.0529304404135566,0,0,0,0,0,0,0,0,0,0,0,0,0.289596390303526,0,0,0,0.0715236385554987,0.0365854662911725,0.00717552039999697,0,0.114910867366072,0.031895734489288,0,0.0692698083236478,0.0764305931706906,0.0480053095083702,0,0,0,0,0.0345911734289274,0,0.135547100918658,0.0422321663740982,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0102101834763503,0.0242538736058389,0,0,0,0,0,0,0,0,0,0,0,0.0308400180034701,0,0,0,0,0,0,0,0,0,0,0,0,0,0 | |coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.807750064546741,0.255756213076752,0.0492195847878491,0,0,0.226549106464441,0.059030951624688,0,0.105542750219401,0,0.170315527999688,0.399372339351466,0.266885070731364,0.0354470656487682,0.0411126530948397,0,0,0,0,0,0,0,0.177265236423641,0.0448571360466903,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0673620022139481,0.623163448471331,0.525389071779607,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0.690431795733084,0,0,0,0,0,0,0.00929149311320963,0,0.110319863569628,0,0,0,0,0,0,0,0.26362597042982,0,0,0.0981416444525993,0,0,0,0,0,0,0,0,0.137740408373976,0.0557366836621885,0,0,0,0,0,0,0,0.0324800223754608,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.423588899072447,0.0597835716559411,0,0,0,0,0,0,0,0,0,0,0,0.236365378443992,0.156026744954718,0.0788703512227347,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0758280215703709,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0.0635717028550276,0,0.120215008744062,0.0659019793256198,0.128841727545421,0.0586723554240733,0,0,0,0.10582914506561,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111946496400116,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0915514965999916,0.0413241580819028,0.0444296048711423,0.0816590655834685,0,0,0,0,0.111087966368681,0,0.362345599751448,0,0,0.138850957170371,0.104960908225686,0.163625352771192,0.263205259864131,0.056886356216389,0.108515345882914,0,0,0,0.0428191061329876,0,0,0,0,0,0.0529304404135566,0,0,0,0,0,0,0,0,0,0,0,0,0.289596390303526,0,0,0,0.0715236385554987,0.0365854662911725,0.00717552039999697,0,0.114910867366072,0.031895734489288,0,0.0692698083236478,0.0764305931706906,0.0480053095083702,0,0,0,0,0.0345911734289274,0,0.135547100918658,0.0422321663740982,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0102101834763503,0.0242538736058389,0,0,0,0,0,0,0,0,0,0,0,0.0308400180034701,0,0,0,0,0,0,0,0,0,0,0,0,0,0 | ||
|gostat_on_MCL_coexpression=GO:0016316;phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity;0.0014243843614358;234515!GO:0048016;inositol phosphate-mediated signaling;0.0014243843614358;234515!GO:0042577;lipid phosphatase activity;0.00474690731086939;234515!GO:0004437;inositol or phosphatidylinositol phosphatase activity;0.0106746882961752;234515!GO:0048015;phosphoinositide-mediated signaling;0.0125201602109508;234515!GO:0019932;second-messenger-mediated signaling;0.0291030877646777;234515!GO:0016791;phosphoric monoester hydrolase activity;0.0455040859357957;234515! | |gostat_on_MCL_coexpression=GO:0016316;phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity;0.0014243843614358;234515!GO:0048016;inositol phosphate-mediated signaling;0.0014243843614358;234515!GO:0042577;lipid phosphatase activity;0.00474690731086939;234515!GO:0004437;inositol or phosphatidylinositol phosphatase activity;0.0106746882961752;234515!GO:0048015;phosphoinositide-mediated signaling;0.0125201602109508;234515!GO:0019932;second-messenger-mediated signaling;0.0291030877646777;234515!GO:0016791;phosphoric monoester hydrolase activity;0.0455040859357957;234515! | ||
|ontology_enrichment_celltype=CL:0000838!1.25e-08!12;CL:0000791!7.40e-08!9;CL:0000789!7.40e-08!9;CL:0002420!7.40e-08!9;CL:0002419!7.40e-08!9;CL:0000790!7.40e-08!9;CL:0000542!8.38e-08!13;CL:0000051!8.38e-08!13;CL:0000084!1.08e-07!11;CL:0000827!1.08e-07!11;CL:0002031!2.12e-07!25 | |||
|ontology_enrichment_disease= | |||
|ontology_enrichment_uberon=UBERON:0000077!7.01e-13!35;UBERON:0004177!1.20e-09!29;UBERON:0005057!1.20e-09!29;UBERON:0002193!8.05e-09!48;UBERON:0002405!8.05e-09!48;UBERON:0002390!1.46e-08!45;UBERON:0003061!1.46e-08!45;UBERON:0004119!2.80e-08!118;UBERON:0000925!2.80e-08!118;UBERON:0006595!2.80e-08!118;UBERON:0004921!1.36e-07!114;UBERON:0001007!2.67e-07!116;UBERON:0001555!2.67e-07!116;UBERON:0007026!2.67e-07!116;UBERON:0000065!4.91e-07!41;UBERON:0002370!7.30e-07!23;UBERON:0000974!7.30e-07!23;UBERON:0004807!7.30e-07!23;UBERON:0005058!7.30e-07!23;UBERON:0003351!7.30e-07!23;UBERON:0009113!7.30e-07!23;UBERON:0003295!7.30e-07!23;UBERON:0009722!7.30e-07!23;UBERON:0005562!7.30e-07!23;UBERON:0007690!7.30e-07!23;UBERON:0001004!9.29e-07!42 | |||
}} | }} | ||
Revision as of 19:45, 11 October 2012
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr1:162722898..162722912,- | p13@Rabgap1l |
| Mm9::chr2:69929983..69929988,+ | p@chr2:69929983..69929988 + |
| Mm9::chr8:84297004..84297019,+ | p13@Inpp4b |
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:0016316 | phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity | 0.0014243843614358 |
| GO:0048016 | inositol phosphate-mediated signaling | 0.0014243843614358 |
| GO:0042577 | lipid phosphatase activity | 0.00474690731086939 |
| GO:0004437 | inositol or phosphatidylinositol phosphatase activity | 0.0106746882961752 |
| GO:0048015 | phosphoinositide-mediated signaling | 0.0125201602109508 |
| GO:0019932 | second-messenger-mediated signaling | 0.0291030877646777 |
| GO:0016791 | phosphoric monoester hydrolase activity | 0.0455040859357957 |
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 |
|---|---|---|
| lymphoid lineage restricted progenitor cell | 1.25e-08 | 12 |
| mature alpha-beta T cell | 7.40e-08 | 9 |
| alpha-beta T cell | 7.40e-08 | 9 |
| immature T cell | 7.40e-08 | 9 |
| mature T cell | 7.40e-08 | 9 |
| immature alpha-beta T cell | 7.40e-08 | 9 |
| lymphocyte | 8.38e-08 | 13 |
| common lymphoid progenitor | 8.38e-08 | 13 |
| T cell | 1.08e-07 | 11 |
| pro-T cell | 1.08e-07 | 11 |
| hematopoietic lineage restricted progenitor cell | 2.12e-07 | 25 |
| Ontology term | p-value | n |
|---|---|---|
| mixed endoderm/mesoderm-derived structure | 7.01e-13 | 35 |
| hemopoietic organ | 1.20e-09 | 29 |
| immune organ | 1.20e-09 | 29 |
| hemolymphoid system | 8.05e-09 | 48 |
| immune system | 8.05e-09 | 48 |
| hematopoietic system | 1.46e-08 | 45 |
| blood island | 1.46e-08 | 45 |
| endoderm-derived structure | 2.80e-08 | 118 |
| endoderm | 2.80e-08 | 118 |
| presumptive endoderm | 2.80e-08 | 118 |
| subdivision of digestive tract | 1.36e-07 | 114 |
| digestive system | 2.67e-07 | 116 |
| digestive tract | 2.67e-07 | 116 |
| primitive gut | 2.67e-07 | 116 |
| respiratory tract | 4.91e-07 | 41 |
| thymus | 7.30e-07 | 23 |
| neck | 7.30e-07 | 23 |
| respiratory system epithelium | 7.30e-07 | 23 |
| hemolymphoid system gland | 7.30e-07 | 23 |
| pharyngeal epithelium | 7.30e-07 | 23 |
| thymic region | 7.30e-07 | 23 |
| pharyngeal gland | 7.30e-07 | 23 |
| entire pharyngeal arch endoderm | 7.30e-07 | 23 |
| thymus primordium | 7.30e-07 | 23 |
| early pharyngeal endoderm | 7.30e-07 | 23 |
| respiratory system | 9.29e-07 | 42 |
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}}} |
