Coexpression cluster:C33: Difference between revisions
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|ontology_enrichment_disease=DOID:1240!3.71e-09!39;DOID:8692!4.62e-08!31;DOID:2531!9.48e-08!51;DOID:0060083!9.48e-08!51 | |ontology_enrichment_disease=DOID:1240!3.71e-09!39;DOID:8692!4.62e-08!31;DOID:2531!9.48e-08!51;DOID:0060083!9.48e-08!51 | ||
|ontology_enrichment_uberon=UBERON:0007023!2.02e-38!115;UBERON:0001049!5.01e-10!57;UBERON:0005068!5.01e-10!57;UBERON:0006241!5.01e-10!57;UBERON:0007135!5.01e-10!57;UBERON:0000178!3.27e-09!15;UBERON:0000179!3.27e-09!15;UBERON:0000463!3.27e-09!15;UBERON:0001017!2.36e-08!82;UBERON:0003080!2.90e-08!42;UBERON:0002780!3.62e-08!41;UBERON:0001890!3.62e-08!41;UBERON:0006240!3.62e-08!41;UBERON:0005743!3.92e-08!86;UBERON:0000955!2.57e-07!69;UBERON:0006238!2.57e-07!69;UBERON:0002616!2.76e-07!59;UBERON:0000073!4.48e-07!94;UBERON:0001016!4.48e-07!94 | |ontology_enrichment_uberon=UBERON:0007023!2.02e-38!115;UBERON:0001049!5.01e-10!57;UBERON:0005068!5.01e-10!57;UBERON:0006241!5.01e-10!57;UBERON:0007135!5.01e-10!57;UBERON:0000178!3.27e-09!15;UBERON:0000179!3.27e-09!15;UBERON:0000463!3.27e-09!15;UBERON:0001017!2.36e-08!82;UBERON:0003080!2.90e-08!42;UBERON:0002780!3.62e-08!41;UBERON:0001890!3.62e-08!41;UBERON:0006240!3.62e-08!41;UBERON:0005743!3.92e-08!86;UBERON:0000955!2.57e-07!69;UBERON:0006238!2.57e-07!69;UBERON:0002616!2.76e-07!59;UBERON:0000073!4.48e-07!94;UBERON:0001016!4.48e-07!94 | ||
|pathway_enrichment=9.22138271824498e-12;1.94571175354969e-09;8;43;Porphyrin and chlorophyll metabolism (KEGG):00860!2.08288425612642e-05;0.00219744289021337;16;1138;Metabolic pathways (KEGG):01100!0.000511027248880248;0.0404350310676496;4;88;Hematopoietic cell lineage (KEGG):04640!7.14094409490062e-08;1.13005440301802e-05;6;51;Malaria (KEGG):05144!6.53990436376727e-16;2.06987973113234e-13;7;9;Heme Biosynthesis (Wikipathways):WP561!2.11138182772082e-16;1.33650469694728e-13;8;14;Metabolism of porphyrins (Reactome):REACT_9431!0.000275342340048467;0.0248988144643828;11;740;TGF beta receptor down reg. targets (Netpath):NetPath_7!8.29717954254321e-06;0.00105042293008597;3;10;{SPTAN1,10} (Static Module):NA | |||
}} | }} | ||
Revision as of 15:01, 13 July 2012
Full id: C33_Reticulocytes_liver_Whole_blood_chronic_acute_spleen
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 9.22138271824498e-12 | 1.94571175354969e-09 | 8 | 43 | Porphyrin and chlorophyll metabolism (KEGG):00860 |
| 2.08288425612642e-05 | 0.00219744289021337 | 16 | 1138 | Metabolic pathways (KEGG):01100 |
| 0.000511027248880248 | 0.0404350310676496 | 4 | 88 | Hematopoietic cell lineage (KEGG):04640 |
| 7.14094409490062e-08 | 1.13005440301802e-05 | 6 | 51 | Malaria (KEGG):05144 |
| 6.53990436376727e-16 | 2.06987973113234e-13 | 7 | 9 | Heme Biosynthesis (Wikipathways):WP561 |
| 2.11138182772082e-16 | 1.33650469694728e-13 | 8 | 14 | Metabolism of porphyrins (Reactome):REACT_9431 |
| 0.000275342340048467 | 0.0248988144643828 | 11 | 740 | TGF beta receptor down reg. targets (Netpath):NetPath_7 |
| 8.29717954254321e-06 | 0.00105042293008597 | 3 | 10 | {SPTAN1,10} (Static Module):NA |
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:0006783 | heme biosynthetic process | 1.99301273996344e-11 |
| GO:0042168 | heme metabolic process | 6.68600696204504e-11 |
| GO:0006779 | porphyrin biosynthetic process | 2.72998340136117e-10 |
| GO:0006778 | porphyrin metabolic process | 6.85167401916645e-10 |
| GO:0033014 | tetrapyrrole biosynthetic process | 6.85167401916645e-10 |
| GO:0033013 | tetrapyrrole metabolic process | 1.86280090892107e-09 |
| GO:0046148 | pigment biosynthetic process | 2.43251010679236e-09 |
| GO:0042440 | pigment metabolic process | 5.50879751734238e-09 |
| GO:0019748 | secondary metabolic process | 2.72264079333764e-08 |
| GO:0046483 | heterocycle metabolic process | 6.03642816456225e-07 |
| GO:0005344 | oxygen transporter activity | 1.50494060027449e-06 |
| GO:0005833 | hemoglobin complex | 1.67539254610695e-06 |
| GO:0015671 | oxygen transport | 2.23168958313686e-06 |
| GO:0015669 | gas transport | 2.73199423140941e-06 |
| GO:0005506 | iron ion binding | 2.73199423140941e-06 |
| GO:0031967 | organelle envelope | 2.43106574620517e-05 |
| GO:0031975 | envelope | 2.43106574620517e-05 |
| GO:0005740 | mitochondrial envelope | 4.20460765065696e-05 |
| GO:0019825 | oxygen binding | 4.20460765065696e-05 |
| GO:0044445 | cytosolic part | 8.98422710584717e-05 |
| GO:0005737 | cytoplasm | 0.000105287408832692 |
| GO:0051188 | cofactor biosynthetic process | 0.000207837484422942 |
| GO:0044459 | plasma membrane part | 0.000207837484422942 |
| GO:0044424 | intracellular part | 0.000248295305902869 |
| GO:0051186 | cofactor metabolic process | 0.000383172372369166 |
| GO:0005887 | integral to plasma membrane | 0.000415172962574889 |
| GO:0044429 | mitochondrial part | 0.000423869175566482 |
| GO:0031226 | intrinsic to plasma membrane | 0.000443705444906324 |
| GO:0044464 | cell part | 0.000754002661362958 |
| GO:0044444 | cytoplasmic part | 0.000801548385687883 |
| GO:0065008 | regulation of biological quality | 0.000976024217327778 |
| GO:0051693 | actin filament capping | 0.000976024217327778 |
| GO:0051016 | barbed-end actin filament capping | 0.000976024217327778 |
| GO:0030835 | negative regulation of actin filament depolymerization | 0.00109447769973282 |
| GO:0005624 | membrane fraction | 0.0011540491141374 |
| GO:0030834 | regulation of actin filament depolymerization | 0.0011540491141374 |
| GO:0030042 | actin filament depolymerization | 0.0011540491141374 |
| GO:0005886 | plasma membrane | 0.00130458001373231 |
| GO:0030863 | cortical cytoskeleton | 0.00141564946523099 |
| GO:0005758 | mitochondrial intermembrane space | 0.0019530118453805 |
| GO:0043249 | erythrocyte maturation | 0.00205489340237058 |
| GO:0000267 | cell fraction | 0.00208594207054039 |
| GO:0031970 | organelle envelope lumen | 0.00247634860687214 |
| GO:0005200 | structural constituent of cytoskeleton | 0.00279739668773175 |
| GO:0005381 | iron ion transmembrane transporter activity | 0.00279739668773175 |
| GO:0030218 | erythrocyte differentiation | 0.00279739668773175 |
| GO:0032502 | developmental process | 0.00337877197355728 |
| GO:0048821 | erythrocyte development | 0.00367137887040516 |
| GO:0031966 | mitochondrial membrane | 0.00479118163273406 |
| GO:0020037 | heme binding | 0.00487295442951012 |
| GO:0046906 | tetrapyrrole binding | 0.00487295442951012 |
| GO:0005622 | intracellular | 0.00487295442951012 |
| GO:0051248 | negative regulation of protein metabolic process | 0.00506034393527609 |
| GO:0022892 | substrate-specific transporter activity | 0.00506034393527609 |
| GO:0051234 | establishment of localization | 0.00516955196778364 |
| GO:0015695 | organic cation transport | 0.00534895534949763 |
| GO:0008064 | regulation of actin polymerization and/or depolymerization | 0.00534895534949763 |
| GO:0005829 | cytosol | 0.00543251356633307 |
| GO:0006800 | oxygen and reactive oxygen species metabolic process | 0.00543251356633307 |
| GO:0044448 | cell cortex part | 0.00543251356633307 |
| GO:0051261 | protein depolymerization | 0.00561170583673194 |
| GO:0030832 | regulation of actin filament length | 0.00561170583673194 |
| GO:0044425 | membrane part | 0.00568771963053565 |
| GO:0032535 | regulation of cellular component size | 0.00568771963053565 |
| GO:0032956 | regulation of actin cytoskeleton organization and biogenesis | 0.00568771963053565 |
| GO:0008091 | spectrin | 0.00568771963053565 |
| GO:0016020 | membrane | 0.00698386154566733 |
| GO:0019866 | organelle inner membrane | 0.00724488380031426 |
| GO:0051129 | negative regulation of cellular component organization and biogenesis | 0.00724488380031426 |
| GO:0042744 | hydrogen peroxide catabolic process | 0.00772730554134139 |
| GO:0006810 | transport | 0.00772730554134139 |
| GO:0033043 | regulation of organelle organization and biogenesis | 0.00850164725875491 |
| GO:0051493 | regulation of cytoskeleton organization and biogenesis | 0.00850164725875491 |
| GO:0005515 | protein binding | 0.00850164725875491 |
| GO:0016634 | oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor | 0.00850164725875491 |
| GO:0042743 | hydrogen peroxide metabolic process | 0.00850164725875491 |
| GO:0006826 | iron ion transport | 0.00850164725875491 |
| GO:0043233 | organelle lumen | 0.00878441285894738 |
| GO:0031974 | membrane-enclosed lumen | 0.00878441285894738 |
| GO:0055082 | cellular chemical homeostasis | 0.00914692040576412 |
| GO:0006873 | cellular ion homeostasis | 0.00914692040576412 |
| GO:0008154 | actin polymerization and/or depolymerization | 0.00973362701208481 |
| GO:0044446 | intracellular organelle part | 0.00981894218394624 |
| GO:0044422 | organelle part | 0.0101512408973475 |
| GO:0005739 | mitochondrion | 0.0102069425801395 |
| GO:0005938 | cell cortex | 0.0106736002878567 |
| GO:0030864 | cortical actin cytoskeleton | 0.0113703490443073 |
| GO:0004601 | peroxidase activity | 0.0117809984242118 |
| GO:0016684 | oxidoreductase activity, acting on peroxide as acceptor | 0.0117809984242118 |
| GO:0031224 | intrinsic to membrane | 0.0123472028152336 |
| GO:0050801 | ion homeostasis | 0.0138239647507748 |
| GO:0051179 | localization | 0.0144483134599268 |
| GO:0008015 | blood circulation | 0.0144483134599268 |
| GO:0003013 | circulatory system process | 0.0144483134599268 |
| GO:0030097 | hemopoiesis | 0.0146266923650598 |
| GO:0042542 | response to hydrogen peroxide | 0.0161479756610863 |
| GO:0030099 | myeloid cell differentiation | 0.0161479756610863 |
| GO:0048534 | hemopoietic or lymphoid organ development | 0.0184353641029009 |
| GO:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | 0.0190937679542153 |
| GO:0048770 | pigment granule | 0.0190937679542153 |
| GO:0042470 | melanosome | 0.0190937679542153 |
| GO:0031090 | organelle membrane | 0.0190937679542153 |
| GO:0015629 | actin cytoskeleton | 0.0191623001355296 |
| GO:0006996 | organelle organization and biogenesis | 0.020315135267643 |
| GO:0048878 | chemical homeostasis | 0.0204845883251409 |
| GO:0002520 | immune system development | 0.0204845883251409 |
| GO:0008092 | cytoskeletal protein binding | 0.0213026801330949 |
| GO:0016021 | integral to membrane | 0.0216266365579753 |
| GO:0005743 | mitochondrial inner membrane | 0.0221192997666714 |
| GO:0004900 | erythropoietin receptor activity | 0.0221192997666714 |
| GO:0018130 | heterocycle biosynthetic process | 0.0221192997666714 |
| GO:0048075 | positive regulation of eye pigmentation | 0.0221192997666714 |
| GO:0006701 | progesterone biosynthetic process | 0.0221192997666714 |
| GO:0009589 | detection of UV | 0.0221192997666714 |
| GO:0001692 | histamine metabolic process | 0.0221192997666714 |
| GO:0045199 | maintenance of epithelial cell polarity | 0.0221192997666714 |
| GO:0004096 | catalase activity | 0.0221192997666714 |
| GO:0000114 | G1-specific transcription in mitotic cell cycle | 0.0221192997666714 |
| GO:0042602 | flavin reductase activity | 0.0221192997666714 |
| GO:0004729 | protoporphyrinogen oxidase activity | 0.0221192997666714 |
| GO:0048250 | mitochondrial iron ion transport | 0.0221192997666714 |
| GO:0048073 | regulation of eye pigmentation | 0.0221192997666714 |
| GO:0004418 | hydroxymethylbilane synthase activity | 0.0221192997666714 |
| GO:0048087 | positive regulation of pigmentation | 0.0221192997666714 |
| GO:0001694 | histamine biosynthetic process | 0.0221192997666714 |
| GO:0045575 | basophil activation | 0.0221192997666714 |
| GO:0030507 | spectrin binding | 0.0221192997666714 |
| GO:0000302 | response to reactive oxygen species | 0.0221192997666714 |
| GO:0007275 | multicellular organismal development | 0.0223352171334581 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0253281589284812 |
| GO:0000041 | transition metal ion transport | 0.0264252931433188 |
| GO:0046915 | transition metal ion transmembrane transporter activity | 0.0264252931433188 |
| GO:0005856 | cytoskeleton | 0.0267354800758849 |
| GO:0007599 | hemostasis | 0.0281774795693257 |
| GO:0019725 | cellular homeostasis | 0.0368427354278818 |
| GO:0006979 | response to oxidative stress | 0.0368427354278818 |
| GO:0065007 | biological regulation | 0.0368427354278818 |
| GO:0004998 | transferrin receptor activity | 0.0368427354278818 |
| GO:0006345 | loss of chromatin silencing | 0.0368427354278818 |
| GO:0008198 | ferrous iron binding | 0.0368427354278818 |
| GO:0004655 | porphobilinogen synthase activity | 0.0368427354278818 |
| GO:0051300 | spindle pole body organization and biogenesis | 0.0368427354278818 |
| GO:0035090 | maintenance of apical/basal cell polarity | 0.0368427354278818 |
| GO:0004074 | biliverdin reductase activity | 0.0368427354278818 |
| GO:0006780 | uroporphyrinogen III biosynthetic process | 0.0368427354278818 |
| GO:0030011 | maintenance of cell polarity | 0.0368427354278818 |
| GO:0048070 | regulation of pigmentation during development | 0.0368427354278818 |
| GO:0046502 | uroporphyrinogen III metabolic process | 0.0368427354278818 |
| GO:0004572 | mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity | 0.0368427354278818 |
| GO:0008379 | thioredoxin peroxidase activity | 0.0368427354278818 |
| GO:0005638 | lamin filament | 0.0368427354278818 |
| GO:0007100 | mitotic centrosome separation | 0.0368427354278818 |
| GO:0005049 | nuclear export signal receptor activity | 0.0368427354278818 |
| GO:0051015 | actin filament binding | 0.0379056072344673 |
| GO:0043229 | intracellular organelle | 0.0381134703512828 |
| GO:0043226 | organelle | 0.0382794173081687 |
| GO:0050878 | regulation of body fluid levels | 0.0390266973317785 |
| GO:0007015 | actin filament organization | 0.0407243480411943 |
| GO:0022603 | regulation of anatomical structure morphogenesis | 0.0418813479437632 |
| GO:0022604 | regulation of cell morphogenesis | 0.0418813479437632 |
| GO:0008360 | regulation of cell shape | 0.0418813479437632 |
| GO:0048469 | cell maturation | 0.0472857370786174 |
| GO:0008375 | acetylglucosaminyltransferase activity | 0.0472857370786174 |
| GO:0042827 | platelet dense granule | 0.047431010983356 |
| GO:0016699 | oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor | 0.047431010983356 |
| GO:0016695 | oxidoreductase activity, acting on hydrogen as donor | 0.047431010983356 |
| GO:0008519 | ammonium transmembrane transporter activity | 0.047431010983356 |
| GO:0004853 | uroporphyrinogen decarboxylase activity | 0.047431010983356 |
| GO:0031304 | intrinsic to mitochondrial inner membrane | 0.047431010983356 |
| GO:0015879 | carnitine transport | 0.047431010983356 |
| GO:0015226 | carnitine transporter activity | 0.047431010983356 |
| GO:0004656 | procollagen-proline 4-dioxygenase activity | 0.047431010983356 |
| GO:0008901 | ferredoxin hydrogenase activity | 0.047431010983356 |
| GO:0004109 | coproporphyrinogen oxidase activity | 0.047431010983356 |
| GO:0031545 | peptidyl-proline 4-dioxygenase activity | 0.047431010983356 |
| GO:0019987 | negative regulation of anti-apoptosis | 0.047431010983356 |
| GO:0051299 | centrosome separation | 0.047431010983356 |
| GO:0015696 | ammonium transport | 0.047431010983356 |
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 |
|---|---|---|
| myeloid cell | 9.62e-08 | 112 |
| common myeloid progenitor | 9.62e-08 | 112 |
| Ontology term | p-value | n |
|---|---|---|
| adult organism | 2.02e-38 | 115 |
| neural tube | 5.01e-10 | 57 |
| neural rod | 5.01e-10 | 57 |
| future spinal cord | 5.01e-10 | 57 |
| neural keel | 5.01e-10 | 57 |
| blood | 3.27e-09 | 15 |
| haemolymphatic fluid | 3.27e-09 | 15 |
| organism substance | 3.27e-09 | 15 |
| central nervous system | 2.36e-08 | 82 |
| anterior neural tube | 2.90e-08 | 42 |
| regional part of forebrain | 3.62e-08 | 41 |
| forebrain | 3.62e-08 | 41 |
| future forebrain | 3.62e-08 | 41 |
| brain | 2.57e-07 | 69 |
| future brain | 2.57e-07 | 69 |
| regional part of brain | 2.76e-07 | 59 |
| regional part of nervous system | 4.48e-07 | 94 |
| nervous system | 4.48e-07 | 94 |
| Ontology term | p-value | n |
|---|---|---|
| leukemia | 3.71e-09 | 39 |
| myeloid leukemia | 4.62e-08 | 31 |
| hematologic cancer | 9.48e-08 | 51 |
| immune system cancer | 9.48e-08 | 51 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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
"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.
