Coexpression cluster:C32: Difference between revisions
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|ontology_enrichment_celltype= | |ontology_enrichment_celltype= | ||
|ontology_enrichment_disease= | |ontology_enrichment_disease= | ||
|ontology_enrichment_uberon=UBERON:0001017! | |ontology_enrichment_uberon=UBERON:0001049!2.69e-143!56;UBERON:0005068!2.69e-143!56;UBERON:0006241!2.69e-143!56;UBERON:0007135!2.69e-143!56;UBERON:0000073!2.72e-132!53;UBERON:0002616!2.72e-132!53;UBERON:0002780!5.62e-114!41;UBERON:0001890!5.62e-114!41;UBERON:0003080!5.62e-114!41;UBERON:0006240!5.62e-114!41;UBERON:0000955!7.76e-105!68;UBERON:0006238!7.76e-105!68;UBERON:0001017!1.79e-104!81;UBERON:0003528!1.32e-102!34;UBERON:0002020!1.32e-102!34;UBERON:0001893!1.04e-101!34;UBERON:0003075!2.10e-95!82;UBERON:0007284!2.10e-95!82;UBERON:0001869!5.04e-95!32;UBERON:0002791!6.67e-95!32;UBERON:0001016!2.65e-93!89;UBERON:0002346!1.42e-90!86;UBERON:0002619!3.90e-79!22;UBERON:0003056!1.84e-74!61;UBERON:0010371!2.17e-73!104;UBERON:0001950!4.10e-71!20;UBERON:0000956!2.38e-69!25;UBERON:0000203!2.38e-69!25;UBERON:0007023!9.65e-61!114;UBERON:0010314!8.73e-59!132;UBERON:0004121!1.05e-44!171;UBERON:0000924!1.05e-44!171;UBERON:0006601!1.05e-44!171;UBERON:0000025!1.81e-35!192;UBERON:0011216!1.96e-35!223;UBERON:0002420!1.52e-34!9;UBERON:0007245!1.52e-34!9;UBERON:0010009!1.52e-34!9;UBERON:0010011!1.52e-34!9;UBERON:0000454!1.52e-34!9;UBERON:0000125!2.63e-34!9;UBERON:0002308!2.63e-34!9;UBERON:0003076!6.47e-29!15;UBERON:0003057!6.47e-29!15;UBERON:0009663!8.24e-27!7;UBERON:0004111!1.96e-26!240;UBERON:0000200!7.91e-24!6;UBERON:0002298!1.09e-22!6;UBERON:0000349!1.24e-20!5;UBERON:0001871!1.54e-20!6;UBERON:0002021!7.41e-20!5;UBERON:0001872!1.10e-19!5;UBERON:0004733!1.94e-19!12;UBERON:0002028!1.94e-19!12;UBERON:0007277!1.94e-19!12;UBERON:0000483!1.31e-18!306;UBERON:0000119!2.48e-18!309;UBERON:0004732!7.63e-18!13;UBERON:0000064!2.27e-17!218;UBERON:0000477!2.69e-17!373;UBERON:0000369!2.59e-16!4;UBERON:0002435!2.59e-16!4;UBERON:0000204!2.59e-16!4;UBERON:0010082!2.59e-16!4;UBERON:0002784!4.67e-16!4;UBERON:0000481!1.35e-14!342;UBERON:0001894!1.00e-13!7;UBERON:0006222!1.00e-13!7;UBERON:0005383!5.02e-13!3;UBERON:0005382!5.02e-13!3;UBERON:0001870!9.53e-13!3;UBERON:0000988!1.79e-12!3;UBERON:0002240!3.62e-12!3;UBERON:0005174!3.62e-12!3;UBERON:0001137!3.62e-12!3;UBERON:0001896!5.74e-12!3;UBERON:0005290!5.74e-12!3;UBERON:0010096!5.74e-12!3;UBERON:0002680!9.28e-11!9;UBERON:0001895!9.28e-11!9;UBERON:0010092!9.28e-11!9;UBERON:0001954!1.30e-09!2;UBERON:0003022!1.30e-09!2;UBERON:0002421!1.30e-09!2;UBERON:0002600!1.30e-09!2;UBERON:0002771!1.41e-09!2;UBERON:0001876!1.81e-09!2;UBERON:0002702!1.97e-09!2;UBERON:0000062!2.17e-09!503;UBERON:0001873!2.41e-09!2;UBERON:0010122!2.41e-09!2;UBERON:0002148!3.20e-09!2;UBERON:0006331!3.20e-09!2;UBERON:0009662!3.20e-09!2;UBERON:0001897!4.25e-09!2;UBERON:0010225!4.25e-09!2;UBERON:0001875!4.99e-09!2;UBERON:0006514!4.99e-09!2;UBERON:0001905!1.14e-08!2;UBERON:0002757!1.14e-08!2;UBERON:0010134!1.14e-08!2;UBERON:0005408!1.14e-08!2;UBERON:0001899!1.14e-08!2;UBERON:0000923!4.61e-08!560;UBERON:0010316!4.61e-08!560;UBERON:0005291!4.61e-08!560;UBERON:0006598!4.61e-08!560;UBERON:0010317!4.61e-08!560;UBERON:0002532!4.61e-08!560;UBERON:0002050!6.25e-08!564;UBERON:0005423!2.17e-07!581;UBERON:0000922!4.68e-07!592 | ||
|pathway_enrichment=3.72272907161102e-05;0.00589121875582444;4;70;Long-term potentiation (KEGG):04720!0.000374195842150392;0.0349085237192865;4;127;Neurotrophin signaling pathway (KEGG):04722!2.22394323770237e-05;0.004692520231552;5;126;Glutamatergic synapse (KEGG):04724!0.000386034227543453;0.0349085237192865;3;53;Amyotrophic lateral sclerosis (ALS) (KEGG):05014!2.22777458562538e-08;7.05090656350432e-06;5;32;Hypothetical Network for Drug Addiction (Wikipathways):WP666!1.7558460710147e-13;1.11145056295231e-10;12;197;Synaptic Transmission (Reactome):REACT_13685!5.66290647761691e-05;0.007169239600663;3;28;{DLG4,28} (Static Module):NA!0.000612612655922707;0.0484729763998842;3;62;{VAMP2,63} (Static Module):NA | |pathway_enrichment=3.72272907161102e-05;0.00589121875582444;4;70;Long-term potentiation (KEGG):04720!0.000374195842150392;0.0349085237192865;4;127;Neurotrophin signaling pathway (KEGG):04722!2.22394323770237e-05;0.004692520231552;5;126;Glutamatergic synapse (KEGG):04724!0.000386034227543453;0.0349085237192865;3;53;Amyotrophic lateral sclerosis (ALS) (KEGG):05014!2.22777458562538e-08;7.05090656350432e-06;5;32;Hypothetical Network for Drug Addiction (Wikipathways):WP666!1.7558460710147e-13;1.11145056295231e-10;12;197;Synaptic Transmission (Reactome):REACT_13685!5.66290647761691e-05;0.007169239600663;3;28;{DLG4,28} (Static Module):NA!0.000612612655922707;0.0484729763998842;3;62;{VAMP2,63} (Static Module):NA | ||
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Revision as of 14:53, 19 October 2012
Full id: C32_middle_occipital_parietal_hippocampus_amygdala_medial_olfactory
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 |
---|---|---|---|---|
3.72272907161102e-05 | 0.00589121875582444 | 4 | 70 | Long-term potentiation (KEGG):04720 |
0.000374195842150392 | 0.0349085237192865 | 4 | 127 | Neurotrophin signaling pathway (KEGG):04722 |
2.22394323770237e-05 | 0.004692520231552 | 5 | 126 | Glutamatergic synapse (KEGG):04724 |
0.000386034227543453 | 0.0349085237192865 | 3 | 53 | Amyotrophic lateral sclerosis (ALS) (KEGG):05014 |
2.22777458562538e-08 | 7.05090656350432e-06 | 5 | 32 | Hypothetical Network for Drug Addiction (Wikipathways):WP666 |
1.7558460710147e-13 | 1.11145056295231e-10 | 12 | 197 | Synaptic Transmission (Reactome):REACT_13685 |
5.66290647761691e-05 | 0.007169239600663 | 3 | 28 | {DLG4,28} (Static Module):NA |
0.000612612655922707 | 0.0484729763998842 | 3 | 62 | {VAMP2,63} (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:0019226 | transmission of nerve impulse | 4.11970715131463e-08 |
GO:0007268 | synaptic transmission | 1.18223541803613e-07 |
GO:0030054 | cell junction | 2.19561803575896e-07 |
GO:0005737 | cytoplasm | 1.91636556988227e-06 |
GO:0007267 | cell-cell signaling | 8.07259504187349e-06 |
GO:0005886 | plasma membrane | 1.17828013672902e-05 |
GO:0005515 | protein binding | 3.83129556296829e-05 |
GO:0043005 | neuron projection | 5.63051401628746e-05 |
GO:0044456 | synapse part | 6.52161821543537e-05 |
GO:0016043 | cellular component organization and biogenesis | 6.52161821543537e-05 |
GO:0044459 | plasma membrane part | 0.000119641958905172 |
GO:0007154 | cell communication | 0.000143913781287093 |
GO:0006810 | transport | 0.000172752868885445 |
GO:0045055 | regulated secretory pathway | 0.000203868023858537 |
GO:0032501 | multicellular organismal process | 0.00025306764177429 |
GO:0051234 | establishment of localization | 0.000253702741825236 |
GO:0048489 | synaptic vesicle transport | 0.0002576314755112 |
GO:0045045 | secretory pathway | 0.000352097194016528 |
GO:0004971 | alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity | 0.00044510766702295 |
GO:0045211 | postsynaptic membrane | 0.00045261252526854 |
GO:0032940 | secretion by cell | 0.00100368057151545 |
GO:0005875 | microtubule associated complex | 0.00102122653690221 |
GO:0051179 | localization | 0.00109676536795504 |
GO:0008066 | glutamate receptor activity | 0.0011643944279613 |
GO:0050877 | neurological system process | 0.0011754844836695 |
GO:0003008 | system process | 0.00136034830346464 |
GO:0044464 | cell part | 0.00140403919526592 |
GO:0004970 | ionotropic glutamate receptor activity | 0.00140403919526592 |
GO:0016020 | membrane | 0.00140403919526592 |
GO:0048488 | synaptic vesicle endocytosis | 0.00140403919526592 |
GO:0051649 | establishment of cellular localization | 0.00146144386627683 |
GO:0005234 | extracellular-glutamate-gated ion channel activity | 0.00148741503143035 |
GO:0007269 | neurotransmitter secretion | 0.00155705658001209 |
GO:0051641 | cellular localization | 0.00164183567742181 |
GO:0044430 | cytoskeletal part | 0.00178419250775785 |
GO:0007399 | nervous system development | 0.00180431423578326 |
GO:0044424 | intracellular part | 0.00194344869082689 |
GO:0051261 | protein depolymerization | 0.0019687653857663 |
GO:0015277 | kainate selective glutamate receptor activity | 0.0019687653857663 |
GO:0005856 | cytoskeleton | 0.0019687653857663 |
GO:0046903 | secretion | 0.00212090933743072 |
GO:0051129 | negative regulation of cellular component organization and biogenesis | 0.00268994276373637 |
GO:0005516 | calmodulin binding | 0.00313323489463127 |
GO:0016192 | vesicle-mediated transport | 0.00341161927712404 |
GO:0016358 | dendrite development | 0.00408664012451171 |
GO:0048731 | system development | 0.00503802729592645 |
GO:0005874 | microtubule | 0.0050695976825352 |
GO:0003001 | generation of a signal involved in cell-cell signaling | 0.00568177636343514 |
GO:0005231 | excitatory extracellular ligand-gated ion channel activity | 0.00595850367133848 |
GO:0042995 | cell projection | 0.00595850367133848 |
GO:0005624 | membrane fraction | 0.00595850367133848 |
GO:0000267 | cell fraction | 0.00595850367133848 |
GO:0007010 | cytoskeleton organization and biogenesis | 0.00597435816286946 |
GO:0048167 | regulation of synaptic plasticity | 0.00615991244761055 |
GO:0044425 | membrane part | 0.00638902147348436 |
GO:0001505 | regulation of neurotransmitter levels | 0.00659725918934219 |
GO:0022836 | gated channel activity | 0.00659725918934219 |
GO:0048856 | anatomical structure development | 0.00709480562738791 |
GO:0050803 | regulation of synapse structure and activity | 0.00716973308865751 |
GO:0007215 | glutamate signaling pathway | 0.00963933297673052 |
GO:0031114 | regulation of microtubule depolymerization | 0.0102479699658883 |
GO:0007026 | negative regulation of microtubule depolymerization | 0.0102479699658883 |
GO:0007019 | microtubule depolymerization | 0.010859174087704 |
GO:0031111 | negative regulation of microtubule polymerization or depolymerization | 0.010859174087704 |
GO:0051128 | regulation of cellular component organization and biogenesis | 0.011874588041324 |
GO:0000226 | microtubule cytoskeleton organization and biogenesis | 0.0123825431470716 |
GO:0051248 | negative regulation of protein metabolic process | 0.0129000075744568 |
GO:0005887 | integral to plasma membrane | 0.0136447383310912 |
GO:0031226 | intrinsic to plasma membrane | 0.0146059498173882 |
GO:0006887 | exocytosis | 0.0148903851146261 |
GO:0031110 | regulation of microtubule polymerization or depolymerization | 0.0155868290915192 |
GO:0031109 | microtubule polymerization or depolymerization | 0.0187049807121038 |
GO:0005622 | intracellular | 0.0188312976011204 |
GO:0031997 | N-terminal myristoylation domain binding | 0.0188312976011204 |
GO:0004423 | iduronate-2-sulfatase activity | 0.0188312976011204 |
GO:0006713 | glucocorticoid catabolic process | 0.0188312976011204 |
GO:0006904 | vesicle docking during exocytosis | 0.0197314628383698 |
GO:0005524 | ATP binding | 0.0206495960893486 |
GO:0005230 | extracellular ligand-gated ion channel activity | 0.0211677278861464 |
GO:0019717 | synaptosome | 0.0212724294997173 |
GO:0005216 | ion channel activity | 0.0212819565169379 |
GO:0048519 | negative regulation of biological process | 0.0212819565169379 |
GO:0032559 | adenyl ribonucleotide binding | 0.0212819565169379 |
GO:0031175 | neurite development | 0.0212819565169379 |
GO:0022838 | substrate specific channel activity | 0.0212819565169379 |
GO:0022406 | membrane docking | 0.0212819565169379 |
GO:0048278 | vesicle docking | 0.0212819565169379 |
GO:0050767 | regulation of neurogenesis | 0.0212819565169379 |
GO:0030425 | dendrite | 0.0212819565169379 |
GO:0022803 | passive transmembrane transporter activity | 0.0215172526455428 |
GO:0015267 | channel activity | 0.0215172526455428 |
GO:0007610 | behavior | 0.022520472305911 |
GO:0065008 | regulation of biological quality | 0.0225569859449941 |
GO:0015629 | actin cytoskeleton | 0.0225829825318049 |
GO:0048869 | cellular developmental process | 0.0231021599550583 |
GO:0030154 | cell differentiation | 0.0231021599550583 |
GO:0043234 | protein complex | 0.0248905908470528 |
GO:0007611 | learning and/or memory | 0.0258078795596219 |
GO:0048666 | neuron development | 0.0264991653251529 |
GO:0007017 | microtubule-based process | 0.0264991653251529 |
GO:0015630 | microtubule cytoskeleton | 0.0268896656957014 |
GO:0050774 | negative regulation of dendrite morphogenesis | 0.0277624714956418 |
GO:0016188 | synaptic vesicle maturation | 0.0277624714956418 |
GO:0030554 | adenyl nucleotide binding | 0.0288912323159971 |
GO:0022834 | ligand-gated channel activity | 0.0296741309567209 |
GO:0015276 | ligand-gated ion channel activity | 0.0296741309567209 |
GO:0015075 | ion transmembrane transporter activity | 0.0319766472832417 |
GO:0007165 | signal transduction | 0.0360012641888821 |
GO:0007275 | multicellular organismal development | 0.0372615071586081 |
GO:0035253 | ciliary rootlet | 0.0372615071586081 |
GO:0035259 | glucocorticoid receptor binding | 0.0372615071586081 |
GO:0048814 | regulation of dendrite morphogenesis | 0.0372615071586081 |
GO:0006431 | methionyl-tRNA aminoacylation | 0.0372615071586081 |
GO:0016595 | glutamate binding | 0.0372615071586081 |
GO:0016081 | synaptic vesicle docking during exocytosis | 0.0372615071586081 |
GO:0019992 | diacylglycerol binding | 0.0386807161842859 |
GO:0030705 | cytoskeleton-dependent intracellular transport | 0.043989855887725 |
GO:0048523 | negative regulation of cellular process | 0.0445060422480017 |
GO:0008324 | cation transmembrane transporter activity | 0.0445060422480017 |
GO:0004157 | dihydropyrimidinase activity | 0.0445060422480017 |
GO:0004825 | methionine-tRNA ligase activity | 0.0445060422480017 |
GO:0050773 | regulation of dendrite development | 0.0445060422480017 |
GO:0031958 | corticosteroid receptor signaling pathway | 0.0445060422480017 |
GO:0048813 | dendrite morphogenesis | 0.0445060422480017 |
GO:0042921 | glucocorticoid receptor signaling pathway | 0.0445060422480017 |
GO:0045745 | positive regulation of G-protein coupled receptor protein signaling pathway | 0.0445060422480017 |
GO:0048858 | cell projection morphogenesis | 0.0445060422480017 |
GO:0032990 | cell part morphogenesis | 0.0445060422480017 |
GO:0030030 | cell projection organization and biogenesis | 0.0445060422480017 |
GO:0009100 | glycoprotein metabolic process | 0.0464483936285055 |
GO:0005509 | calcium ion binding | 0.0464483936285055 |
GO:0030182 | neuron differentiation | 0.0470654319998472 |
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><br>uberon_data<br><br>
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