Coexpression cluster:C682: Difference between revisions
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{{Coexpression_clusters | {{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0159895489336821,0,0.0164525096832193,0,0,0,0,0,0,0.850098845283701,0.370981480737826,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.440903172569491,0.631122157134778,0.564491809947528,0.642777535919522,0.597438235261667,0.518383600367654,0.561599759654322,0.586830403682648,0.381342479821279,0.483043410756561,0.44858037261087,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0408118974110906,0.0848314897427103,0.0640322205040047,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0464009723343685,0.07481925209622,0,0,0,0,0,0,0.263343091623509,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.504927398066512,0,0,0.0955771563476108,0,0,0,0,0.0204283766509788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.18655229194125,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0402022792589852,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.174979787616842,0,0.642961961895772,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0473659963914933,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.175686944807253,0.146415578970277,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.445508389219647,0.0300822291072195,0,0,0,0,0,0,0,0,0,0.176036802110703,0.12076093114532|full_id=C682_Burkitt_lymphoma_CD19_appendix_tonsil_spleen_diffuse|gostat_on_coexpression_clusters=GO:0008310!single-stranded DNA specific 3'-5' exodeoxyribonuclease activity!0.0101844084028938!3669$GO:0008859!exoribonuclease II activity!0.0101844084028938!3669$GO:0005232!serotonin-activated cation-selective channel activity!0.0101844084028938!3359$GO:0008297!single-stranded DNA specific exodeoxyribonuclease activity!0.0101844084028938!3669$GO:0008296!3'-5'-exodeoxyribonuclease activity!0.0122207504459862!3669$GO:0000738!DNA catabolic process, exonucleolytic!0.0135780120329791!3669$GO:0016895!exodeoxyribonuclease activity, producing 5'-phosphomonoesters!0.0187936840949419!3669$GO:0004529!exodeoxyribonuclease activity!0.0187936840949419!3669$GO:0043285!biopolymer catabolic process!0.0187936840949419!84447;3669$GO:0030433!ER-associated protein catabolic process!0.0187936840949419!84447$GO:0006515!misfolded or incompletely synthesized protein catabolic process!0.0187936840949419!84447$GO:0044265!cellular macromolecule catabolic process!0.0187936840949419!84447;3669$GO:0000175!3'-5'-exoribonuclease activity!0.0187936840949419!3669$GO:0004993!serotonin receptor activity!0.0189047164366943!3359$GO:0016896!exoribonuclease activity, producing 5'-phosphomonoesters!0.019014415156573!3669$GO:0004532!exoribonuclease activity!0.019014415156573!3669$GO:0016605!PML body!0.019014415156573!3669$GO:0009057!macromolecule catabolic process!0.019014415156573!84447;3669$GO:0016796!exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters!0.0234024274421159!3669$GO:0043161!proteasomal ubiquitin-dependent protein catabolic process!0.0234024274421159!84447$GO:0008408!3'-5' exonuclease activity!0.0258852662218033!3669$GO:0044248!cellular catabolic process!0.0258852662218033!84447;3669$GO:0006308!DNA catabolic process!0.0309508886207327!3669$GO:0009056!catabolic process!0.0341070749707598!84447;3669$GO:0006401!RNA catabolic process!0.0374058692672204!3669$GO:0004536!deoxyribonuclease activity!0.0390878569504989!3669$GO:0044446!intracellular organelle 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Latest revision as of 11:28, 17 September 2013
Full id: C682_Burkitt_lymphoma_CD19_appendix_tonsil_spleen_diffuse
Phase1 CAGE Peaks
| Hg19::chr11:113848216..113848228,+ | p2@HTR3A |
| Hg19::chr11:64900812..64900834,- | p5@SYVN1 |
| Hg19::chr12:27977018..27977041,- | p@chr12:27977018..27977041 - |
| Hg19::chr12:32418225..32418236,+ | p@chr12:32418225..32418236 + |
| Hg19::chr15:89191020..89191067,+ | p13@ISG20 |
| Hg19::chr1:155953595..155953599,- | p@chr1:155953595..155953599 - |
| Hg19::chr20:43214306..43214347,- | p@chr20:43214306..43214347 - |
| Hg19::chr20:57698461..57698483,+ | p@chr20:57698461..57698483 + |
| Hg19::chr22:22398325..22398339,- | p1@PRAMEL |
| Hg19::chr2:220142973..220142983,- | p26@TUBA4A |
| Hg19::chr2:65257848..65257867,+ | p@chr2:65257848..65257867 + |
| Hg19::chr2:65257873..65257887,+ | p@chr2:65257873..65257887 + |
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
No results for this coexpression
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0008310 | single-stranded DNA specific 3'-5' exodeoxyribonuclease activity | 0.0101844084028938 |
| GO:0008859 | exoribonuclease II activity | 0.0101844084028938 |
| GO:0005232 | serotonin-activated cation-selective channel activity | 0.0101844084028938 |
| GO:0008297 | single-stranded DNA specific exodeoxyribonuclease activity | 0.0101844084028938 |
| GO:0008296 | 3'-5'-exodeoxyribonuclease activity | 0.0122207504459862 |
| GO:0000738 | DNA catabolic process, exonucleolytic | 0.0135780120329791 |
| GO:0016895 | exodeoxyribonuclease activity, producing 5'-phosphomonoesters | 0.0187936840949419 |
| GO:0004529 | exodeoxyribonuclease activity | 0.0187936840949419 |
| GO:0043285 | biopolymer catabolic process | 0.0187936840949419 |
| GO:0030433 | ER-associated protein catabolic process | 0.0187936840949419 |
| GO:0006515 | misfolded or incompletely synthesized protein catabolic process | 0.0187936840949419 |
| GO:0044265 | cellular macromolecule catabolic process | 0.0187936840949419 |
| GO:0000175 | 3'-5'-exoribonuclease activity | 0.0187936840949419 |
| GO:0004993 | serotonin receptor activity | 0.0189047164366943 |
| GO:0016896 | exoribonuclease activity, producing 5'-phosphomonoesters | 0.019014415156573 |
| GO:0004532 | exoribonuclease activity | 0.019014415156573 |
| GO:0016605 | PML body | 0.019014415156573 |
| GO:0009057 | macromolecule catabolic process | 0.019014415156573 |
| GO:0016796 | exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters | 0.0234024274421159 |
| GO:0043161 | proteasomal ubiquitin-dependent protein catabolic process | 0.0234024274421159 |
| GO:0008408 | 3'-5' exonuclease activity | 0.0258852662218033 |
| GO:0044248 | cellular catabolic process | 0.0258852662218033 |
| GO:0006308 | DNA catabolic process | 0.0309508886207327 |
| GO:0009056 | catabolic process | 0.0341070749707598 |
| GO:0006401 | RNA catabolic process | 0.0374058692672204 |
| GO:0004536 | deoxyribonuclease activity | 0.0390878569504989 |
| GO:0044446 | intracellular organelle part | 0.0403333517367145 |
| GO:0044422 | organelle part | 0.0403333517367145 |
| GO:0008227 | amine receptor activity | 0.0469240956780526 |
| GO:0004527 | exonuclease activity | 0.0471621932387917 |
| GO:0005231 | excitatory extracellular ligand-gated ion channel activity | 0.0471621932387917 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| lymphocyte of B lineage | 2.37e-93 | 24 |
| pro-B cell | 2.37e-93 | 24 |
| B cell | 4.93e-69 | 14 |
| lymphocyte | 2.98e-44 | 53 |
| common lymphoid progenitor | 2.98e-44 | 53 |
| nucleate cell | 1.76e-42 | 55 |
| lymphoid lineage restricted progenitor cell | 8.62e-41 | 52 |
| nongranular leukocyte | 7.05e-24 | 115 |
| leukocyte | 1.91e-19 | 136 |
| single nucleate cell | 2.82e-17 | 3 |
| mononuclear cell | 2.82e-17 | 3 |
| hematopoietic lineage restricted progenitor cell | 4.52e-15 | 120 |
| hematopoietic stem cell | 8.30e-15 | 168 |
| angioblastic mesenchymal cell | 8.30e-15 | 168 |
| hematopoietic cell | 8.36e-14 | 177 |
| mature B cell | 2.57e-12 | 2 |
| pre-B-II cell | 2.57e-12 | 2 |
| transitional stage B cell | 2.57e-12 | 2 |
| small pre-B-II cell | 2.57e-12 | 2 |
| immature B cell | 2.57e-12 | 2 |
| hematopoietic oligopotent progenitor cell | 1.89e-11 | 161 |
| hematopoietic multipotent progenitor cell | 1.89e-11 | 161 |
| circulating cell | 6.67e-09 | 6 |
| precursor B cell | 1.68e-08 | 3 |
| B-1 B cell | 4.06e-07 | 1 |
| antibody secreting cell | 7.29e-07 | 1 |
| plasma cell | 7.29e-07 | 1 |
| plasmablast | 7.29e-07 | 1 |
| Ontology term | p-value | n |
|---|---|---|
| blood | 4.29e-09 | 15 |
| haemolymphatic fluid | 4.29e-09 | 15 |
| organism substance | 4.29e-09 | 15 |
| spleen | 1.44e-08 | 3 |
| gastrointestinal system mesentery | 1.44e-08 | 3 |
| stomach region | 1.44e-08 | 3 |
| mesentery | 1.44e-08 | 3 |
| gastrointestinal system serosa | 1.44e-08 | 3 |
| mesentery of stomach | 1.44e-08 | 3 |
| gut mesentery | 1.44e-08 | 3 |
| dorsal mesentery | 1.44e-08 | 3 |
| dorsal mesogastrium | 1.44e-08 | 3 |
| peritoneal cavity | 1.44e-08 | 3 |
| spleen primordium | 1.44e-08 | 3 |
| vermiform appendix | 2.52e-07 | 1 |
| caecum | 2.52e-07 | 1 |
| midgut | 2.52e-07 | 1 |
| tonsil | 3.01e-07 | 1 |
| mucosa-associated lymphoid tissue | 3.01e-07 | 1 |
| lymphoid tissue | 3.01e-07 | 1 |
| tonsillar ring | 3.01e-07 | 1 |
| lymph node | 4.85e-07 | 1 |
| Ontology term | p-value | n |
|---|---|---|
| lymphoma | 8.76e-10 | 10 |
| acute leukemia | 3.82e-07 | 1 |
| lymphatic system cancer | 4.06e-07 | 1 |
| lymphosarcoma | 4.06e-07 | 1 |
| genetic disease | 5.45e-07 | 1 |
| monogenic disease | 5.45e-07 | 1 |
| xeroderma pigmentosum | 5.45e-07 | 1 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<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 | 0.00251029 |
| MA0004.1 | 0.32225 |
| MA0006.1 | 0.188769 |
| MA0007.1 | 0.305951 |
| MA0009.1 | 0.756202 |
| MA0014.1 | 0.00141144 |
| MA0017.1 | 1.8359 |
| MA0019.1 | 0.45566 |
| MA0024.1 | 0.654931 |
| MA0025.1 | 0.886436 |
| MA0027.1 | 2.35633 |
| MA0028.1 | 0.201461 |
| MA0029.1 | 0.673506 |
| MA0030.1 | 0.662482 |
| MA0031.1 | 0.600685 |
| MA0038.1 | 1.87299 |
| MA0040.1 | 0.67914 |
| MA0041.1 | 3.36019 |
| MA0042.1 | 2.30218 |
| MA0043.1 | 0.756508 |
| MA0046.1 | 0.745626 |
| MA0048.1 | 0.155795 |
| MA0050.1 | 0.311321 |
| MA0051.1 | 0.410316 |
| MA0052.1 | 1.63439 |
| MA0055.1 | 0.107116 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0373953 |
| MA0058.1 | 0.676094 |
| MA0059.1 | 0.239727 |
| MA0060.1 | 0.103131 |
| MA0061.1 | 0.0856761 |
| MA0063.1 | 0 |
| MA0066.1 | 0.414559 |
| MA0067.1 | 1.06751 |
| MA0068.1 | 0.226673 |
| MA0069.1 | 0.741884 |
| MA0070.1 | 0.731026 |
| MA0071.1 | 0.379038 |
| MA0072.1 | 0.726666 |
| MA0073.1 | 0.00012619 |
| MA0074.1 | 1.05467 |
| MA0076.1 | 0.254045 |
| MA0077.1 | 0.719193 |
| MA0078.1 | 0.502027 |
| MA0081.1 | 0.239862 |
| MA0083.1 | 0.763502 |
| MA0084.1 | 1.25286 |
| MA0087.1 | 0.724294 |
| MA0088.1 | 0.654005 |
| MA0089.1 | 0 |
| MA0090.1 | 0.734839 |
| MA0091.1 | 0.86696 |
| MA0092.1 | 0.291716 |
| MA0093.1 | 0.558691 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.426863 |
| MA0101.1 | 0.19375 |
| MA0103.1 | 1.02503 |
| MA0105.1 | 0.130274 |
| MA0106.1 | 0.452066 |
| MA0107.1 | 0.137948 |
| MA0108.2 | 0.597764 |
| MA0109.1 | 0 |
| MA0111.1 | 0.761158 |
| MA0113.1 | 0.467266 |
| MA0114.1 | 0.828144 |
| MA0115.1 | 0.992167 |
| MA0116.1 | 0.140463 |
| MA0117.1 | 0.792789 |
| MA0119.1 | 0.226505 |
| MA0122.1 | 0.818044 |
| MA0124.1 | 0.951337 |
| MA0125.1 | 0.868909 |
| MA0130.1 | 0 |
| MA0131.1 | 0.519055 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.785738 |
| MA0136.1 | 0.420617 |
| MA0139.1 | 0.268952 |
| MA0140.1 | 0.376643 |
| MA0141.1 | 0.670251 |
| MA0142.1 | 2.392 |
| MA0143.1 | 1.17969 |
| MA0144.1 | 0.124153 |
| MA0145.1 | 0.232227 |
| MA0146.1 | 0.00710499 |
| MA0147.1 | 0.143012 |
| MA0148.1 | 0.344198 |
| MA0149.1 | 0.367947 |
| MA0062.2 | 0.0823902 |
| MA0035.2 | 0.376007 |
| MA0039.2 | 7.40554e-05 |
| MA0138.2 | 0.503176 |
| MA0002.2 | 0.316618 |
| MA0137.2 | 0.20663 |
| MA0104.2 | 0.68621 |
| MA0047.2 | 0.440861 |
| MA0112.2 | 0.0192555 |
| MA0065.2 | 0.733267 |
| MA0150.1 | 0.261236 |
| MA0151.1 | 0 |
| MA0152.1 | 0.382565 |
| MA0153.1 | 0.852412 |
| MA0154.1 | 0.5526 |
| MA0155.1 | 0.0793743 |
| MA0156.1 | 0.208455 |
| MA0157.1 | 0.544523 |
| MA0158.1 | 0 |
| MA0159.1 | 0.143477 |
| MA0160.1 | 0.357736 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0188054 |
| MA0163.1 | 0.0909552 |
| MA0164.1 | 0.478818 |
| MA0080.2 | 1.06373 |
| MA0018.2 | 0.453345 |
| MA0099.2 | 0.382887 |
| MA0079.2 | 1.02222e-06 |
| MA0102.2 | 1.28978 |
| MA0258.1 | 0.117513 |
| MA0259.1 | 0.149181 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
No analysis results for this cluster
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
