Coexpression cluster:C27: Difference between revisions
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|pathway_enrichment=9.2343327187409e-06;0.0011690665221926;4;50;Glycerolipid metabolism (KEGG):00561!1.29993107295641e-26;8.2285636918141e-24;17;101;Pancreatic secretion (KEGG):04972!2.63164388643526e-18;8.3291529005676e-16;12;81;Protein digestion and absorption (KEGG):04974!2.31113888153688e-09;4.87650304004282e-07;6;46;Fat digestion and absorption (KEGG):04975!1.42993929566819e-08;2.2628789353949e-06;4;11;{ACY1,11} (Static Module):NA!0.000302346783113562;0.0318975856184808;2;10;{PLG,10} (Static Module):NA | |pathway_enrichment=9.2343327187409e-06;0.0011690665221926;4;50;Glycerolipid metabolism (KEGG):00561!1.29993107295641e-26;8.2285636918141e-24;17;101;Pancreatic secretion (KEGG):04972!2.63164388643526e-18;8.3291529005676e-16;12;81;Protein digestion and absorption (KEGG):04974!2.31113888153688e-09;4.87650304004282e-07;6;46;Fat digestion and absorption (KEGG):04975!1.42993929566819e-08;2.2628789353949e-06;4;11;{ACY1,11} (Static Module):NA!0.000302346783113562;0.0318975856184808;2;10;{PLG,10} (Static Module):NA | ||
|tfbs_overrepresentation=8.02911e-12,0.78745,1,1.41895e-06,0.999999,0.794017,0.996746,1,0.0198979,0.830757,0.00699863,1,0.913479,0.0467531,0.173663,0.0871541,0.999496,0.0121572,0.00339071,0.997617,0.813631,0.999993,0.0756363,6.04865e-05,0.984803,0.972252,0.999692,0.896903,0.0365283,0.823538,0.999996,0.804912,0.912558,0.884713,0.968855,0.0985187,1,0.280037,0.91239,0.763771,0.204058,0.00184915,0.198657,0.599355,0.987064,0.963799,0.496477,0.440628,0.325028,0.366003,0.542213,0.363648,0.276402,0.916032,0.754345,0.377813,0.113441,0.889102,0.727895,0.0472368,0.998721,0.823143,0.278318,0.000340874,0.875827,0.00397404,0.737315,0.722755,1,0.966268,0.739615,0.495882,0.972959,0.402968,0.812396,0.739131,0.580694,0.999484,0.999789,0.802735,0.723601,0.959878,0.999335,0.0126534,0.999999,1,0.999027,0.103694,1,0.989225,0.933706,0.996205,0.999543,0.999764,0.521204,0.323894,1,0.965694,0.151711,0.998639,0.990598,0.381351,0.971077,0.844511,0.999979,0.99991,0.970631,1.993e-06,0.893255,0.374503,1,0.367493,0.720797,0.36709,0.592472,0.498195,0.0441915,0.748838,0.743981,0.0923259,0.000434914,0.999996,0.0076789,0.529761,0.374567,0.814219,0.99441,0.645285,0.974651,0.999449,0.982907,0.978188,0.906423,0.994143,0.918895,0.982279,0.879342,0.995345,0.86738,0.586778,0.994129,0.0270029,0.849464,0.0455973,1,0.634291,0.923869,0.974248,0.0669049,0.879796,0.854658,0.693031,0.00226157,0.00141818,0.987447,0.968605,0.999995,0.831794,0.519693,0.497278,0.932427,0.137918,0.999716,0.0541338,0.996601,0.000567164,0.948661,0.981312,0.316232,0.999998,0.048166,0.999976,0.999998,0.470959,0.994998,0.776266,0.995725,8.74129e-10,0.570253,0.999694,0.02252,0.999999,0.740432,0.910613,0.804228,0.955889,0.999568,0.994449,0.465869,0.981501,0.999938,0.753524,0.998608,0.0177096,0.841437,0.128558,0.0740342,0.999472,0.59636,0.995966,0.000126094,0.320062,0.167859,0.820406,0.503341,0.922718,0.434796,0.999984,0.898453,1,0.717576,1,0.882702,0.656074,0.972524,0.81542,0.997444,0.93754,0.976197,0.702748,0.00415052,0.995181,0.940548,0.531057,0.994928,0.743642,1,0.999931,0.1122,0.999432,0.99916,1,0.837423,0.602374,0.325191,0.948509,0.74869,1,0.999594,8.36575e-08,0.000510132,1,0.234144,0.0147515,0.417448,5.28061e-08,0.148785,0.087367,1,0.920928,0.0161612,0.00407144,0.102328,0.043764,0.229163,0.0636198,2.11591e-10,0.790305,0.541503,1,0.999999,0.63612,0.997177,0.999882,0.996496,0.000557687,0.519218,0.999728,0.52666,0.391999,1,0.998827,0.999912,1,0.93904,0.75944,1.32337e-15,0.997151,1,0.999995,1,0.231975,1,1,2.13153e-09,0.155543,1,0.93686,0.000691054,0.999973,0.50375,0.000111434,0.0557094,0.893531,0.437888,0.120096,0.988004,0.517551,0.998471,0.991155,0.632444,0.107529,0.974096,0.0078427,0.155318,1.17987e-22,0.958633,0.581404,0.67181,0.200492,0.189333,1.29625e-07,1,0.00982388,1,0.0989711,0.505098,0.999634,0.0533511,7.9618e-05,0.269529,1.0439e-06,0.0491459,0.38262,0.0129087,1,0.999945,1.1851e-11,0.272506,5.24091e-06,0.0253468,0.991392,0.00489386,9.42445e-11,0.954,0.10434,0.970891,0.000141499,1,0.999528,1,1,1,1,9.96991e-09,0.999697,0.0301771,0.999904,0.0400872,0.00699655,2.21234e-06,0.813658,0.530417,2.60345e-05,0.986181,0.0355503,0.0353053,0.480659,0.999288,0.0739434,1,1,0.992264,1,0.728031,2.24821e-07,0.731114,0.00573635,0.876237,0.991879,0.981635,0.887275,0.563309,3.72546e-05,1,0.465893,0.999995,0.994232,0.932809,0.999837,0.995233,0.93268,1,0.0847616,1,0.000251468,0.890161,0.0013046,0.999988,0.580062,1,1.91415e-09,0.0653794,3.34057e-06,0.00649287,1,0.970061,0.0406491,0.0311992,0.857098,0.136707,0.993604,1.2437e-05,0.201373,0.00131715,0.998359,1.00317e-06,7.2334e-13,0.999999,0.0968295,1.52323e-08,0.245988,0.0718431,3.01825e-09,0.844277,4.25619e-07,0.350237,0.198025,0.54204,0.964335,0.899238,0.00725086,0.0185748,0.999755,0.00304285,1.2657e-10,0.926464,1,0.957316,0.999999,0.999999,0.802613,1.36865e-06,0.652758,0.999988,0.283441,0.996406,0.194302,1,0.26936,0.0251411,0.196474,0.0323869,0.000388211,0.973275,0.803161,1,0.989497,3.13935e-11,6.75569e-08,0.284149,1.8407e-06,0.000691253,0.00120847,1,0.78263,0.959349,0.987591,1,0.912281,0.999816,5.66195e-06,0.990698,0.00196429,0.933606,1,0.229661,0.945685,0.891229,0.999466,0.996473,0.462872,0.225975,0.994194,0.999959,0.207283,1,0.766289,0.99999,0.0023506,1,0.616211,0.999965,0.957848,0.0421849,0.999878,0.980859,0.997587,0.915998,0.999955,0.0578961,0.409535,0.719704,1,0.211175,0.999245,0.117513,0.00154499,0.673267,0.197293,0.99935,6.54587e-12,0.399729,0.905881,0.999845,1,0.541479,0.000779722,1,1,0.999852,0.999992,0.771123,0.99155,0.999953,0.0436612,0.0404797,0.999981,0.999714,0.00496207,0.432264,0.823369,0.00255146,0.998895,2.23253e-09,0.793557,0.537663,2.31736e-13,3.39133e-06,2.22595e-08,0.218561,1.86936e-07,4.52111e-09,1.45927e-22,0.891006,0.809329,1,0.000274335,0.962364,0.888828,0.88207,0.0937266,0.32116,0.398125,0.607146,0.999255,0.805548,0.971142,0.827121,7.65459e-06,0.100655,0.00446637,0.999224,0.999969,0.966543,0.67861,0.996154,1,0.000302963,1,0.426278,0.541733,0.9933,0.999529,2.40388e-05,0.999999,0.999214,0.804106,0.62678,1,0.997465,0.11261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| ||
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}} | }} |
Revision as of 13:08, 26 November 2012
Full id: C27_pancreas_temporal_duodenum_salivary_ductus_umbilical_lung
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 |
---|---|---|---|---|
9.2343327187409e-06 | 0.0011690665221926 | 4 | 50 | Glycerolipid metabolism (KEGG):00561 |
1.29993107295641e-26 | 8.2285636918141e-24 | 17 | 101 | Pancreatic secretion (KEGG):04972 |
2.63164388643526e-18 | 8.3291529005676e-16 | 12 | 81 | Protein digestion and absorption (KEGG):04974 |
2.31113888153688e-09 | 4.87650304004282e-07 | 6 | 46 | Fat digestion and absorption (KEGG):04975 |
1.42993929566819e-08 | 2.2628789353949e-06 | 4 | 11 | {ACY1,11} (Static Module):NA |
0.000302346783113562 | 0.0318975856184808 | 2 | 10 | {PLG,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:0007586 | digestion | 1.44172092772405e-14 |
GO:0016787 | hydrolase activity | 6.08242741039348e-07 |
GO:0008233 | peptidase activity | 1.11682410598755e-06 |
GO:0006508 | proteolysis | 1.93271217139652e-06 |
GO:0004806 | triacylglycerol lipase activity | 2.94578893295425e-06 |
GO:0004252 | serine-type endopeptidase activity | 1.77436343952148e-05 |
GO:0004295 | trypsin activity | 1.77436343952148e-05 |
GO:0016042 | lipid catabolic process | 2.31531230264122e-05 |
GO:0008236 | serine-type peptidase activity | 2.85199605932328e-05 |
GO:0017171 | serine hydrolase activity | 2.85199605932328e-05 |
GO:0008235 | metalloexopeptidase activity | 0.000142159407595542 |
GO:0004263 | chymotrypsin activity | 0.00016556161242981 |
GO:0006641 | triacylglycerol metabolic process | 0.000219528196793056 |
GO:0016298 | lipase activity | 0.00027852553014174 |
GO:0006638 | neutral lipid metabolic process | 0.000384562326290239 |
GO:0006639 | acylglycerol metabolic process | 0.000384562326290239 |
GO:0046486 | glycerolipid metabolic process | 0.000413099613412682 |
GO:0006662 | glycerol ether metabolic process | 0.000442765337828319 |
GO:0004175 | endopeptidase activity | 0.000514426510362401 |
GO:0031638 | zymogen activation | 0.000594595713171037 |
GO:0008238 | exopeptidase activity | 0.000693477334984891 |
GO:0004091 | carboxylesterase activity | 0.000693477334984891 |
GO:0032501 | multicellular organismal process | 0.000828895858251802 |
GO:0000267 | cell fraction | 0.00101000426630287 |
GO:0005615 | extracellular space | 0.00128922563172228 |
GO:0008237 | metallopeptidase activity | 0.0015983179859819 |
GO:0009056 | catabolic process | 0.0015983179859819 |
GO:0004182 | carboxypeptidase A activity | 0.0015983179859819 |
GO:0030299 | cholesterol absorption | 0.00184101507790922 |
GO:0044241 | lipid digestion | 0.00184101507790922 |
GO:0004181 | metallocarboxypeptidase activity | 0.00199505038907144 |
GO:0044267 | cellular protein metabolic process | 0.00268336386548484 |
GO:0050892 | intestinal absorption | 0.00268336386548484 |
GO:0044260 | cellular macromolecule metabolic process | 0.00333909590682858 |
GO:0004180 | carboxypeptidase activity | 0.00577911671323896 |
GO:0019538 | protein metabolic process | 0.0062640150916866 |
GO:0022600 | digestive system process | 0.00899705953090361 |
GO:0044243 | multicellular organismal catabolic process | 0.010732571739735 |
GO:0030902 | hindbrain development | 0.0119554775587876 |
GO:0044236 | multicellular organismal metabolic process | 0.0119554775587876 |
GO:0006829 | zinc ion transport | 0.0119554775587876 |
GO:0044421 | extracellular region part | 0.0203062213875256 |
GO:0005624 | membrane fraction | 0.0205391121211919 |
GO:0006629 | lipid metabolic process | 0.0205391121211919 |
GO:0007039 | vacuolar protein catabolic process | 0.0205391121211919 |
GO:0032023 | trypsinogen activation | 0.0205391121211919 |
GO:0044240 | multicellular organismal lipid catabolic process | 0.0205391121211919 |
GO:0015068 | glycine amidinotransferase activity | 0.0205391121211919 |
GO:0010107 | potassium ion import | 0.0205391121211919 |
GO:0031017 | exocrine pancreas development | 0.0205391121211919 |
GO:0015067 | amidinotransferase activity | 0.0205391121211919 |
GO:0050425 | carboxypeptidase B activity | 0.0205391121211919 |
GO:0044258 | intestinal lipid catabolic process | 0.0205391121211919 |
GO:0030246 | carbohydrate binding | 0.0211062679538568 |
GO:0051179 | localization | 0.0242456807671222 |
GO:0018212 | peptidyl-tyrosine modification | 0.0319192224379496 |
GO:0008476 | protein-tyrosine sulfotransferase activity | 0.0345263356428125 |
GO:0048384 | retinoic acid receptor signaling pathway | 0.0345263356428125 |
GO:0006478 | peptidyl-tyrosine sulfation | 0.0345263356428125 |
GO:0006600 | creatine metabolic process | 0.0345263356428125 |
GO:0018350 | protein amino acid esterification | 0.0345263356428125 |
GO:0006601 | creatine biosynthetic process | 0.0345263356428125 |
GO:0006931 | substrate-bound cell migration, cell attachment to substrate | 0.0345263356428125 |
GO:0004867 | serine-type endopeptidase inhibitor activity | 0.0348102326088066 |
GO:0005529 | sugar binding | 0.0358302781970765 |
GO:0006599 | phosphagen metabolic process | 0.0459121433354091 |
GO:0045779 | negative regulation of bone resorption | 0.0459121433354091 |
GO:0042589 | zymogen granule membrane | 0.0459121433354091 |
GO:0004771 | sterol esterase activity | 0.0459121433354091 |
GO:0042396 | phosphagen biosynthetic process | 0.0459121433354091 |
GO:0005155 | epidermal growth factor receptor activating ligand activity | 0.0459121433354091 |
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>
Ontology term | p-value | n |
---|---|---|
duodenum | 3.27e-23 | 2 |
small intestine | 1.60e-14 | 4 |
temporal lobe | 9.89e-11 | 6 |
pancreas | 5.73e-08 | 10 |
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