Coexpression cluster:C20: Difference between revisions
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|tf_chipseq_enrich=ZNF274#10782;5:9.2082004782782:0.000233591262925649:0.00256611317015797 | |tf_chipseq_enrich=ZNF274#10782;5:9.2082004782782:0.000233591262925649:0.00256611317015797 | ||
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| ||
|tfbs_overrepresentation_for_novel_motifs=0.00120043,4.23965,0.0311408,0.30342,2.14533,0.124584,0.534732,5.35665,0.699905,0.0846364,0.00221397,0.0674067,0.424708,0.531479,0.484627,1.0946,0.04616,1.60101,2.35746,3.14888,1.78024,6.62612,1.85923e-05,0.0743217,0.815902,0.0553515,4.48965,0.0962989,0.674658,3.46236,0.103777,1.82213,0.333367,3.73281,1.17929e-07,4.48857,2.34587e-12,0.666033,1.83524,2.55777,0.880547,0.160561,0.462682,6.17339,1.75014,0.000462438,0.0670344,0.308765,2.50346,0.607876,0.190683,0.0454151,1.62178,0.0660933,0.352428,0.0726372,0.6015,0.462509,1.75935,0.132569,0.304099,0.00321576,1.5556,0.0441991,0.0104635,6.30256e-05,0.121507,0.217081,0.398059,0.0254106,0.000655048,0.053434,3.67125e-09,0.0872796,3.09613e-07,0.59336,4.38664,0.0183001,0.106303,1.57611,0.808661,0.0146396,0.0167219,0.107746,0.000788692,0,0.920184,0.841845,0.0267109,1.38549,0.257894,0.0600882,0.410956,0.175808,0.0298434,2.20771,1.24737,0.00243637,0.0106168,0.439759,0.292913,1.10103,0.348414,0.306836,0.043913,0.00102115,2.85453e-05,0.0617579,0.000126112,0.00449095,1.10529,0.0241945,0.0683171,0.00347082,0.445903,2.9461,1.37111e-06,0.281431,0.00592706,0.0612729,0.0794117,0.634142,0.0502616,0.350193,0.384649,0.465228,0.175586,0.119174,0.315498,1.0928,0.476094,0.567121,1.11303,2.83226,0.440441,0.895876,0.80654,0.738603,0.207941,0.667523,0.0509319,0.0816074,0.419446,0.26226,0.255577,0.27705,3.9236,0.14633,1.6083,0.000732013,1.20157,0,0.167229,0.536875,0.653512,1.16227,0.22463,0.0308921,0.000723219,0.00220528,0.559103,0.867942,0.02415,0.088986,0.31815,2.86037,0.98354,2.80552,0.308866 | |||
}} | }} |
Revision as of 13:06, 26 November 2012
Full id: C20_heart_left_skeletal_diaphragm_tongue_umbilical_throat
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 |
---|---|---|---|---|
0.000231657192529121 | 0.0146639002870933 | 7 | 177 | Calcium signaling pathway (KEGG):04020 |
6.30934046684172e-15 | 7.98762503102162e-13 | 13 | 77 | Cardiac muscle contraction (KEGG):04260 |
1.66943907379131e-17 | 5.28377466854948e-15 | 15 | 83 | Hypertrophic cardiomyopathy (HCM) (KEGG):05410 |
7.88252100001465e-07 | 7.12805113287039e-05 | 7 | 74 | Arrhythmogenic right ventricular cardiomyopathy (ARVC) (KEGG):05412 |
1.80419036842224e-18 | 1.14205250321128e-15 | 16 | 90 | Dilated cardiomyopathy (KEGG):05414 |
3.3423723116765e-05 | 0.00264465209161403 | 4 | 27 | Proteins and DNA Sequences in Cardicac Structures (Wikipathways):WP1550 |
0.00072677724805668 | 0.0353884613861445 | 6 | 155 | Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289 |
2.59780828378785e-17 | 5.48137547879235e-15 | 12 | 39 | Striated Muscle Contraction (Wikipathways):WP383 |
0.000119209861846449 | 0.00838442694986693 | 4 | 37 | Sandbox Pathway (Wikipathways):WP4 |
0.000590865467916936 | 0.0311681534326184 | 6 | 149 | Calcium Regulation in the Cardiac Cell (Wikipathways):WP536 |
1.20381781467267e-12 | 1.27002779447966e-10 | 10 | 49 | Muscle contraction (Reactome):REACT_17044 |
1.05480829310387e-15 | 1.66923412383687e-13 | 21 | 288 | {ACTB,297} (Static Module):NA |
0.000418496897381243 | 0.0240825941856661 | 4 | 51 | {RXRA,51} (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:0006936 | muscle contraction | 1.05751769297081e-28 |
GO:0003012 | muscle system process | 1.05751769297081e-28 |
GO:0005856 | cytoskeleton | 5.44006125812182e-25 |
GO:0044449 | contractile fiber part | 2.84073743440755e-21 |
GO:0030017 | sarcomere | 3.78895651587484e-21 |
GO:0043292 | contractile fiber | 6.07839266221264e-21 |
GO:0030016 | myofibril | 1.51424532702748e-20 |
GO:0008307 | structural constituent of muscle | 2.53002378767014e-20 |
GO:0003008 | system process | 2.75003715235446e-19 |
GO:0005737 | cytoplasm | 5.7727270248596e-19 |
GO:0015629 | actin cytoskeleton | 2.01291352194336e-17 |
GO:0060047 | heart contraction | 6.85273603523471e-16 |
GO:0003015 | heart process | 6.85273603523471e-16 |
GO:0008016 | regulation of heart contraction | 1.12593579305353e-14 |
GO:0007517 | muscle development | 4.26645042493245e-14 |
GO:0006941 | striated muscle contraction | 1.72110638760366e-13 |
GO:0008015 | blood circulation | 5.8757171663596e-12 |
GO:0003013 | circulatory system process | 5.8757171663596e-12 |
GO:0016528 | sarcoplasm | 1.95149340125531e-11 |
GO:0016529 | sarcoplasmic reticulum | 1.95149340125531e-11 |
GO:0051239 | regulation of multicellular organismal process | 5.23736273403332e-11 |
GO:0032501 | multicellular organismal process | 6.32133608835853e-11 |
GO:0008092 | cytoskeletal protein binding | 2.09546324594442e-10 |
GO:0044444 | cytoplasmic part | 2.04736423951825e-09 |
GO:0055008 | cardiac muscle morphogensis | 7.20264568812095e-09 |
GO:0048644 | muscle morphogenesis | 7.20264568812095e-09 |
GO:0031674 | I band | 7.24326329202904e-09 |
GO:0048513 | organ development | 1.34792652690571e-08 |
GO:0043228 | non-membrane-bound organelle | 1.6548641073336e-08 |
GO:0043232 | intracellular non-membrane-bound organelle | 1.6548641073336e-08 |
GO:0033018 | sarcoplasmic reticulum lumen | 2.22118958060532e-08 |
GO:0007507 | heart development | 4.29565772044466e-08 |
GO:0044424 | intracellular part | 5.15478229405041e-08 |
GO:0005859 | muscle myosin complex | 7.96110952820054e-08 |
GO:0016460 | myosin II complex | 1.0011931345007e-07 |
GO:0003779 | actin binding | 2.23959574192018e-07 |
GO:0005515 | protein binding | 2.49536222986095e-07 |
GO:0005863 | striated muscle thick filament | 3.62514518065399e-07 |
GO:0032982 | myosin filament | 3.62514518065399e-07 |
GO:0055010 | ventricular cardiac muscle morphogenesis | 5.9541751059795e-07 |
GO:0044430 | cytoskeletal part | 1.21011431260716e-06 |
GO:0016459 | myosin complex | 1.97354519912282e-06 |
GO:0005790 | smooth endoplasmic reticulum | 7.68066500143272e-06 |
GO:0048856 | anatomical structure development | 1.3570515009947e-05 |
GO:0030018 | Z disc | 1.47253202313085e-05 |
GO:0005622 | intracellular | 2.80860364191816e-05 |
GO:0048731 | system development | 2.8203127372795e-05 |
GO:0030049 | muscle filament sliding | 2.8203127372795e-05 |
GO:0033275 | actin-myosin filament sliding | 2.8203127372795e-05 |
GO:0006937 | regulation of muscle contraction | 3.3938835292669e-05 |
GO:0005861 | troponin complex | 5.39933143552282e-05 |
GO:0043229 | intracellular organelle | 6.42149723950858e-05 |
GO:0005887 | integral to plasma membrane | 6.42149723950858e-05 |
GO:0043226 | organelle | 6.42149723950858e-05 |
GO:0000267 | cell fraction | 6.8368456546819e-05 |
GO:0044446 | intracellular organelle part | 6.8368456546819e-05 |
GO:0044464 | cell part | 6.8368456546819e-05 |
GO:0044422 | organelle part | 7.19920293628092e-05 |
GO:0031226 | intrinsic to plasma membrane | 7.65239996744321e-05 |
GO:0048738 | cardiac muscle development | 7.74361416271956e-05 |
GO:0007512 | adult heart development | 7.74361416271956e-05 |
GO:0002026 | regulation of the force of heart contraction | 7.74361416271956e-05 |
GO:0014706 | striated muscle development | 0.000101166974930067 |
GO:0005624 | membrane fraction | 0.000179457571512481 |
GO:0005865 | striated muscle thin filament | 0.000343075984136097 |
GO:0007275 | multicellular organismal development | 0.000358278264091356 |
GO:0031013 | troponin I binding | 0.000411548223425469 |
GO:0031014 | troponin T binding | 0.000411548223425469 |
GO:0030048 | actin filament-based movement | 0.00106134952044451 |
GO:0051146 | striated muscle cell differentiation | 0.00106134952044451 |
GO:0045822 | negative regulation of heart contraction | 0.00116218590675779 |
GO:0030172 | troponin C binding | 0.00116218590675779 |
GO:0005516 | calmodulin binding | 0.00126742539320808 |
GO:0005509 | calcium ion binding | 0.00181986295583941 |
GO:0004111 | creatine kinase activity | 0.00219473594335477 |
GO:0030898 | actin-dependent ATPase activity | 0.00219473594335477 |
GO:0032502 | developmental process | 0.00236126936422951 |
GO:0042805 | actinin binding | 0.00355228953842855 |
GO:0005788 | endoplasmic reticulum lumen | 0.00427165065362383 |
GO:0006874 | cellular calcium ion homeostasis | 0.00427165065362383 |
GO:0055074 | calcium ion homeostasis | 0.00427165065362383 |
GO:0030029 | actin filament-based process | 0.00493144102952482 |
GO:0007519 | skeletal muscle development | 0.00493144102952482 |
GO:0002027 | regulation of heart rate | 0.00493144102952482 |
GO:0006875 | cellular metal ion homeostasis | 0.00526909936175276 |
GO:0055065 | metal ion homeostasis | 0.00526909936175276 |
GO:0043167 | ion binding | 0.00572324197977719 |
GO:0006512 | ubiquitin cycle | 0.00626802957935771 |
GO:0030371 | translation repressor activity | 0.00626993202379179 |
GO:0055002 | striated muscle cell development | 0.00626993202379179 |
GO:0030239 | myofibril assembly | 0.00626993202379179 |
GO:0055001 | muscle cell development | 0.00626993202379179 |
GO:0009887 | organ morphogenesis | 0.00626993202379179 |
GO:0035051 | cardiac cell differentiation | 0.00808566665778536 |
GO:0006942 | regulation of striated muscle contraction | 0.00808566665778536 |
GO:0005739 | mitochondrion | 0.00819043501349864 |
GO:0007010 | cytoskeleton organization and biogenesis | 0.00862774828988738 |
GO:0044459 | plasma membrane part | 0.00863462056629045 |
GO:0033017 | sarcoplasmic reticulum membrane | 0.0122635369189636 |
GO:0048628 | myoblast maturation | 0.0122635369189636 |
GO:0009653 | anatomical structure morphogenesis | 0.0143858696676094 |
GO:0048627 | myoblast development | 0.0143858696676094 |
GO:0005246 | calcium channel regulator activity | 0.0143858696676094 |
GO:0044432 | endoplasmic reticulum part | 0.0143858696676094 |
GO:0042692 | muscle cell differentiation | 0.0171687207048302 |
GO:0046872 | metal ion binding | 0.0224249166413304 |
GO:0005783 | endoplasmic reticulum | 0.0229890056251833 |
GO:0030005 | cellular di-, tri-valent inorganic cation homeostasis | 0.0229890056251833 |
GO:0055066 | di-, tri-valent inorganic cation homeostasis | 0.024467576897517 |
GO:0000146 | microfilament motor activity | 0.0255867087129621 |
GO:0065007 | biological regulation | 0.0266547663341774 |
GO:0022892 | substrate-specific transporter activity | 0.0291879065851272 |
GO:0022857 | transmembrane transporter activity | 0.0300258334301265 |
GO:0051789 | response to protein stimulus | 0.0320049870436943 |
GO:0006986 | response to unfolded protein | 0.0320049870436943 |
GO:0030003 | cellular cation homeostasis | 0.0336471667869255 |
GO:0022891 | substrate-specific transmembrane transporter activity | 0.0341238420811505 |
GO:0050789 | regulation of biological process | 0.0341238420811505 |
GO:0001570 | vasculogenesis | 0.0341238420811505 |
GO:0055080 | cation homeostasis | 0.0346474849856165 |
GO:0005813 | centrosome | 0.0380427338720723 |
GO:0048878 | chemical homeostasis | 0.0380427338720723 |
GO:0031967 | organelle envelope | 0.0380427338720723 |
GO:0006635 | fatty acid beta-oxidation | 0.0380427338720723 |
GO:0031975 | envelope | 0.0380427338720723 |
GO:0031966 | mitochondrial membrane | 0.0380427338720723 |
GO:0005523 | tropomyosin binding | 0.0380427338720723 |
GO:0031032 | actomyosin structure organization and biogenesis | 0.0380427338720723 |
GO:0046314 | phosphocreatine biosynthetic process | 0.0380427338720723 |
GO:0051370 | ZASP binding | 0.0380427338720723 |
GO:0005477 | pyruvate secondary active transmembrane transporter activity | 0.0380427338720723 |
GO:0055013 | cardiac muscle cell development | 0.0380427338720723 |
GO:0006848 | pyruvate transport | 0.0380427338720723 |
GO:0050080 | malonyl-CoA decarboxylase activity | 0.0380427338720723 |
GO:0051374 | FATZ 1 binding | 0.0380427338720723 |
GO:0043033 | isoamylase complex | 0.0380427338720723 |
GO:0032780 | negative regulation of ATPase activity | 0.0380427338720723 |
GO:0004492 | methylmalonyl-CoA decarboxylase activity | 0.0380427338720723 |
GO:0055003 | cardiac myofibril assembly | 0.0380427338720723 |
GO:0060044 | negative regulation of cardiac muscle cell proliferation | 0.0380427338720723 |
GO:0055009 | atrial cardiac muscle morphogenesis | 0.0380427338720723 |
GO:0015866 | ADP transport | 0.0380427338720723 |
GO:0001980 | ischemic regulation of systemic arterial blood pressure | 0.0380427338720723 |
GO:0060039 | pericardium development | 0.0380427338720723 |
GO:0006603 | phosphocreatine metabolic process | 0.0380427338720723 |
GO:0050833 | pyruvate transmembrane transporter activity | 0.0380427338720723 |
GO:0008267 | poly-glutamine tract binding | 0.0380427338720723 |
GO:0015085 | calcium ion transmembrane transporter activity | 0.0446282503028984 |
GO:0005740 | mitochondrial envelope | 0.0482474283684438 |
GO:0005815 | microtubule organizing center | 0.0490762999901469 |
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>disease_data<br>
Ontology term | p-value | n |
---|---|---|
heart disease | 3.57e-17 | 2 |
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
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
TF | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
ZNF274#10782 | 5 | 9.2082004782782 | 0.000233591262925649 | 0.00256611317015797 |
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