Coexpression cluster:C118: Difference between revisions
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Latest revision as of 10:35, 17 September 2013
Full id: C118_cerebellum_parietal_occipital_medial_middle_frontal_insula
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 |
---|---|---|---|---|
3.21588558482119e-05 | 0.00678551858397271 | 5 | 126 | Glutamatergic synapse (KEGG):04724 |
9.77861502511732e-05 | 0.0123824018731482 | 4 | 83 | Hypertrophic cardiomyopathy (HCM) (KEGG):05410 |
0.000106696491900211 | 0.0123824018731482 | 3 | 32 | Hypothetical Network for Drug Addiction (Wikipathways):WP666 |
2.70775915789819e-10 | 1.71401154694955e-07 | 10 | 197 | Synaptic Transmission (Reactome):REACT_13685 |
0.000470699126992762 | 0.0425646496266312 | 4 | 125 | Integration of energy metabolism (Reactome):REACT_1505 |
0.000117368738134106 | 0.0123824018731482 | 6 | 265 | Axon guidance (Reactome):REACT_18266 |
9.00885823625835e-07 | 0.000285130363177577 | 4 | 26 | {RASGRF1,26} (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:0005886 | plasma membrane | 2.52069622669271e-06 |
GO:0030054 | cell junction | 1.17290317297813e-05 |
GO:0044425 | membrane part | 1.73607675976265e-05 |
GO:0044459 | plasma membrane part | 1.96924833961766e-05 |
GO:0016021 | integral to membrane | 2.96607884633392e-05 |
GO:0031224 | intrinsic to membrane | 2.96607884633392e-05 |
GO:0016020 | membrane | 2.96607884633392e-05 |
GO:0019226 | transmission of nerve impulse | 5.52398222233686e-05 |
GO:0005891 | voltage-gated calcium channel complex | 9.62884579184354e-05 |
GO:0044456 | synapse part | 0.000100003913961408 |
GO:0022836 | gated channel activity | 0.000100003913961408 |
GO:0007268 | synaptic transmission | 0.000195909142086055 |
GO:0005245 | voltage-gated calcium channel activity | 0.000735829937860229 |
GO:0005216 | ion channel activity | 0.000774514386210364 |
GO:0045211 | postsynaptic membrane | 0.000774514386210364 |
GO:0022838 | substrate specific channel activity | 0.000774514386210364 |
GO:0022843 | voltage-gated cation channel activity | 0.000774514386210364 |
GO:0022803 | passive transmembrane transporter activity | 0.000774514386210364 |
GO:0015267 | channel activity | 0.000774514386210364 |
GO:0005509 | calcium ion binding | 0.00232511436195309 |
GO:0022832 | voltage-gated channel activity | 0.00232511436195309 |
GO:0005244 | voltage-gated ion channel activity | 0.00232511436195309 |
GO:0007267 | cell-cell signaling | 0.00232511436195309 |
GO:0050808 | synapse organization and biogenesis | 0.00235257978902726 |
GO:0016079 | synaptic vesicle exocytosis | 0.00325202505564878 |
GO:0007154 | cell communication | 0.00325202505564878 |
GO:0005262 | calcium channel activity | 0.00336573353867295 |
GO:0007528 | neuromuscular junction development | 0.00483663614046024 |
GO:0005261 | cation channel activity | 0.00737641660664985 |
GO:0048489 | synaptic vesicle transport | 0.015006921745046 |
GO:0006816 | calcium ion transport | 0.015006921745046 |
GO:0046873 | metal ion transmembrane transporter activity | 0.0164919554253955 |
GO:0043062 | extracellular structure organization and biogenesis | 0.0166120175719292 |
GO:0005200 | structural constituent of cytoskeleton | 0.0166869234776399 |
GO:0006790 | sulfur metabolic process | 0.0166902838132157 |
GO:0005515 | protein binding | 0.0166902838132157 |
GO:0007215 | glutamate signaling pathway | 0.0168140216446291 |
GO:0044464 | cell part | 0.0192693977562345 |
GO:0008066 | glutamate receptor activity | 0.0194643442025702 |
GO:0006887 | exocytosis | 0.0305731989543396 |
GO:0006810 | transport | 0.0318329478143315 |
GO:0048172 | regulation of short-term neuronal synaptic plasticity | 0.0318329478143315 |
GO:0031557 | induction of programmed cell death in response to chemical stimulus | 0.0318329478143315 |
GO:0015674 | di-, tri-valent inorganic cation transport | 0.0318329478143315 |
GO:0015075 | ion transmembrane transporter activity | 0.0348655253979806 |
GO:0004970 | ionotropic glutamate receptor activity | 0.0399196833593958 |
GO:0006811 | ion transport | 0.0399196833593958 |
GO:0051234 | establishment of localization | 0.0399196833593958 |
GO:0005230 | extracellular ligand-gated ion channel activity | 0.0399196833593958 |
GO:0051179 | localization | 0.0414994901283276 |
GO:0005234 | extracellular-glutamate-gated ion channel activity | 0.0419511124508003 |
GO:0007269 | neurotransmitter secretion | 0.042722762846028 |
GO:0008081 | phosphoric diester hydrolase activity | 0.042722762846028 |
GO:0048741 | skeletal muscle fiber development | 0.0443533759491619 |
GO:0048747 | muscle fiber development | 0.0443533759491619 |
GO:0005856 | cytoskeleton | 0.0443533759491619 |
GO:0030001 | metal ion transport | 0.0443533759491619 |
GO:0006552 | leucine catabolic process | 0.0457689282451179 |
GO:0006768 | biotin metabolic process | 0.0457689282451179 |
GO:0016080 | synaptic vesicle targeting | 0.0457689282451179 |
GO:0004485 | methylcrotonoyl-CoA carboxylase activity | 0.0457689282451179 |
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) |
---|---|
MA0003.1 | 13.2451 |
MA0004.1 | 0.00496355 |
MA0006.1 | 3.53795 |
MA0007.1 | 0.587552 |
MA0009.1 | 0.0388877 |
MA0014.1 | 11.0588 |
MA0017.1 | 0.401652 |
MA0019.1 | 0.0980324 |
MA0024.1 | 0.209026 |
MA0025.1 | 0.581023 |
MA0027.1 | 1.26202 |
MA0028.1 | 0.0141074 |
MA0029.1 | 0.093339 |
MA0030.1 | 0.418709 |
MA0031.1 | 0.147879 |
MA0038.1 | 0.0623951 |
MA0040.1 | 0.239834 |
MA0041.1 | 0.282244 |
MA0042.1 | 0.124598 |
MA0043.1 | 0.632701 |
MA0046.1 | 0.03626 |
MA0048.1 | 4.73454 |
MA0050.1 | 0.207691 |
MA0051.1 | 0.530364 |
MA0052.1 | 0.0992373 |
MA0055.1 | 9.81063 |
MA0056.1 | 0 |
MA0057.1 | 4.17896 |
MA0058.1 | 0.00711556 |
MA0059.1 | 0.00691374 |
MA0060.1 | 0.115344 |
MA0061.1 | 0.216394 |
MA0063.1 | 0 |
MA0066.1 | 0.023972 |
MA0067.1 | 0.500379 |
MA0068.1 | 0.798421 |
MA0069.1 | 0.141138 |
MA0070.1 | 0.132824 |
MA0071.1 | 0.413501 |
MA0072.1 | 0.306304 |
MA0073.1 | 21.7327 |
MA0074.1 | 0.0590845 |
MA0076.1 | 0.000877415 |
MA0077.1 | 0.0301867 |
MA0078.1 | 0.0208972 |
MA0081.1 | 0.18597 |
MA0083.1 | 0.0407684 |
MA0084.1 | 0.77642 |
MA0087.1 | 0.302806 |
MA0088.1 | 0.915528 |
MA0089.1 | 0 |
MA0090.1 | 1.58588 |
MA0091.1 | 0.0835774 |
MA0092.1 | 0.0500079 |
MA0093.1 | 0.00040018 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.259171 |
MA0101.1 | 0.187191 |
MA0103.1 | 0.146766 |
MA0105.1 | 1.16156 |
MA0106.1 | 0.0945562 |
MA0107.1 | 0.0458457 |
MA0108.2 | 0.144905 |
MA0109.1 | 0 |
MA0111.1 | 1.20354 |
MA0113.1 | 0.109763 |
MA0114.1 | 0.148757 |
MA0115.1 | 0.400693 |
MA0116.1 | 0.535387 |
MA0117.1 | 0.411069 |
MA0119.1 | 0.0529522 |
MA0122.1 | 0.454558 |
MA0124.1 | 0.108113 |
MA0125.1 | 0.0740881 |
MA0130.1 | 0 |
MA0131.1 | 0.313346 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.0468355 |
MA0136.1 | 0.00704588 |
MA0139.1 | 2.59291 |
MA0140.1 | 0.265642 |
MA0141.1 | 0.181407 |
MA0142.1 | 0.43205 |
MA0143.1 | 0.357511 |
MA0144.1 | 0.0152101 |
MA0145.1 | 0.570727 |
MA0146.1 | 1.74456 |
MA0147.1 | 0.560948 |
MA0148.1 | 0.189327 |
MA0149.1 | 0.539444 |
MA0062.2 | 0.00270268 |
MA0035.2 | 0.0843735 |
MA0039.2 | 1.32519 |
MA0138.2 | 1.25155 |
MA0002.2 | 0.170947 |
MA0137.2 | 0.00252811 |
MA0104.2 | 0.690544 |
MA0047.2 | 0.084197 |
MA0112.2 | 1.15151 |
MA0065.2 | 0.110249 |
MA0150.1 | 0.101973 |
MA0151.1 | 0 |
MA0152.1 | 0.0913819 |
MA0153.1 | 0.240551 |
MA0154.1 | 1.10394 |
MA0155.1 | 3.42796 |
MA0156.1 | 0.00739187 |
MA0157.1 | 0.36998 |
MA0158.1 | 0 |
MA0159.1 | 0.131321 |
MA0160.1 | 0.128718 |
MA0161.1 | 0 |
MA0162.1 | 13.2821 |
MA0163.1 | 13.1343 |
MA0164.1 | 0.586218 |
MA0080.2 | 0.0014469 |
MA0018.2 | 0.0392078 |
MA0099.2 | 0.0150312 |
MA0079.2 | 37.8476 |
MA0102.2 | 0.31059 |
MA0258.1 | 0.0582441 |
MA0259.1 | 0.293789 |
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
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
TF | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
CTBP2#1488 | 12 | 4.91898041877083 | 7.36337494877413e-06 | 0.000211386343121226 |
CTCF#10664 | 45 | 1.57654599208089 | 0.000837623142862051 | 0.00631902076115066 |
RAD21#5885 | 33 | 2.23343868333372 | 8.74177219459004e-06 | 0.00023597362270116 |
SUZ12#23512 | 10 | 3.27554123601718 | 0.00107559596656458 | 0.00759579195023588 |
ZNF263#10127 | 32 | 1.71960086525714 | 0.00148467697309175 | 0.00949529567622349 |
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