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Coexpression cluster:C215: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!9.70e-13!39;DOID:8692!8.95e-12!31;DOID:2531!7.01e-11!51;DOID:0060083!7.01e-11!51
|ontology_enrichment_disease=DOID:1240!9.70e-13!39;DOID:8692!8.95e-12!31;DOID:2531!7.01e-11!51;DOID:0060083!7.01e-11!51
|ontology_enrichment_uberon=UBERON:0007023!3.17e-15!115;UBERON:0001049!3.84e-09!57;UBERON:0005068!3.84e-09!57;UBERON:0006241!3.84e-09!57;UBERON:0007135!3.84e-09!57;UBERON:0003080!9.85e-08!42;UBERON:0002780!1.66e-07!41;UBERON:0001890!1.66e-07!41;UBERON:0006240!1.66e-07!41;UBERON:0002616!1.99e-07!59;UBERON:0000073!5.93e-07!94;UBERON:0001016!5.93e-07!94
|ontology_enrichment_uberon=UBERON:0007023!3.17e-15!115;UBERON:0001049!3.84e-09!57;UBERON:0005068!3.84e-09!57;UBERON:0006241!3.84e-09!57;UBERON:0007135!3.84e-09!57;UBERON:0003080!9.85e-08!42;UBERON:0002780!1.66e-07!41;UBERON:0001890!1.66e-07!41;UBERON:0006240!1.66e-07!41;UBERON:0002616!1.99e-07!59;UBERON:0000073!5.93e-07!94;UBERON:0001016!5.93e-07!94
|tf_chipseq_enrich=SUZ12#23512;5:3.63157832688862:0.0123545526060442:0.0447305387097916
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0.194269,0.598254,0.998841,0.000527502,0.00692417,0.684314,0.987994,0.998369,0.538621,0.999948,0.996659,0.603947,0.413161,0.994653,0.95046,0.742339,0.747836,0.999061,0.486984,0.987169,0.97244,0.598007,0.878133,0.727957,0.972067,0.903042,0.000257324,0.861943,0.626696,0.972658,0.100242,0.999582,0.543405,0.931212,0.584379,0.945542,0.999916,0.881561,0.970046,0.412112,0.969364,0.0222885,0.999801,0.999584,0.671937,0.899021,0.999981,0.63643,0.843359,0.930014,0.612764,0.628681,1,0.875574,0.706033,0.693288,0.692915,0.431384,0.538902,0.660201,0.480134,0.189801,0.830135,0.469914,0.999996,0.155786,0.919576,0.9846,0.946049,0.95668,0.658954,0.999732,0.744307,0.674208,0.989114,0.423406,0.455221,0.988451,0.81765,0.979918,0.999634,0.203236,0.372286,0.28468,1,1,0.0204513,0.976833,0.490521,0.217583,0.000101546,0.688197,0.901477,0.968492,0.271404,0.291722,0.0556014,0.81287,0.981054,0.53304,0.586735,0.413554,0.653227,0.720489,0.528201,0.077335,0.98713,0.722826,0.926591,0.74178,0.943999,0.837583,0.886797,0.977679,0.993176,0.921229,0.914939,0.207845,0.635009,0.0638194,0.89101,0.438374,0.992437,0.50572,0.990888,0.979676,0.820203,0.381905,0.760437,0.481447,0.0149257,0.681966,0.346653,0.801862,0.957873,0.659231,0.148255,0.498766,0.381741,0.945787,0.866702,0.815957,0.521367,0.936001,0.698319,0.987945,0.40182,0.920933,0.785955,0.96929,0.910861,0.998941,0.919314,0.936691,0.120398,0.609712,0.641963,0.0252107,0.98503,0.952595,0.85809,0.332182,0.200657,0.929783,0.999028,0.753646,0.998548,0.989103,0.921161,0.400678,0.992556,0.999997,0.570572,0.99349,0.109081,0.64011,0.419402,0.96454,0.373121,0.219521,0.980078,0.722193,0.999026,0.978536,0.271474,0.402421,0.611403,0.961548,0.819507,0.339763,0.755933,0.998824,1,0.977674,0.989343,0.990649,0.012979,0.994092,0.804825,0.999851,0.987553,1,1,0.145119,0.908483,0.623128,0.967459,0.00106125,0.998767,0.820809,0.999101,0.95303,0.779692,0.999927,0.259947,0.881305,0.530213,0.957855,0.590996,0.814828,0.292351,0.459994,0.999991,0.970627,0.989776,0.999998,0.381698,0.999983,0.994004,0.79057,1,0.994102,1,0.991989,0.999998,0.999939,0.999996,0.599034,0.887155,0.000406914,0.0411564,0.908283,0.939033,0.999949,0.00255103,0.747443,0.026901,0.56235,0.902222,0.86365,0.990239,0.916504,0.0438197,0.340687,0.647508,0.996147,0.973476,0.182514,0.772344,0.999357,0.999808,0.980579,0.849999,0.0105197,0.999703,0.00445734,0.995728,0.0218884,0.915561,0.999996,0.998742,0.978964,0.0485401,0.691521,0.988081,0.999995,0.95958,0.896409,0.883406,0.857495,0.999997,0.985004,0.744664,0.324017,0.999842,0.999963,0.645776,0.820133,0.982219,0.999352,0.328127,0.818601,0.996266,0.801767,0.892036,0.42445,0.766137,0.600426,0.520763,0.999868,0.989246,0.748284,0.999763,0.842544,0.951816,0.907172,0.604422,0.997741,0.913813,0.999839,0.750467,0.0753199,0.672018,0.829716,0.998765,0.0660797,0.999697,0.961078,0.719148,0.995583,0.977499,0.997971,0.998397,0.152443,0.536954,0.50645,0.946887,0.4521,0.951275,0.936816,0.986499,0.99911,0.231419,0.736223,0.571579,0.999917,0.967884,0.819724,0.998297,0.962995,0.621709,0.434517,0.460925,0.556326,0.979044,0.608038,0.545606,0.530442,0.967803,0.705364,0.820334,0.709109,0.983102,0.717152,0.91507,0.923104,0.447611,0.638302,0.670329,0.405977,0.796157,0.994834,0.965212,0.445178,0.992926,0.665718,0.870992,0.996789,0.979457,0.843693,0.991126,0.920801,0.575583,0.9914,0.95155,0.00245495,0.533322,0.658163,0.807654,0.941891,0.981387,0.979971,0.609261,0.404733,0.995365,0.958304,0.996923,0.798761,0.623017,0.924751,0.0617038,0.701113,0.937777,0.913344,0.0825677,0.985749,0.594597,0.79255,0.708592,0.657781,0.993871,0.965173,0.294616,0.979184,0.792529,0.219068,0.128377,0.756445,0.657078,0.365012,0.676307,0.734305,0.808274,0.537396,0.924098,0.835371,0.762914,0.998931,0.888975,0.116965,0.0882922,0.102674,0.84915,0.515032,0.998971,0.999069,0.994706,0.996046,0.172464,0.467444,0.869573,0.998625,0.774838,0.997119,0.998493,0.987344,0.964176,0.96867,0.568133,0.986898,0.354279,0.626649,0.99892,0.686893,0.987026,0.0845006,0.904161,0.965619,0.998148,0.767808,0.976815,0.861069,0.96556,0.731871,0.71838,0.71953,0.889913,0.845603,0.615666,0.362642,0.976698,0.268185,0.995748,0.206719,0.730681,0.529925,0.857728,0.216102,0.782331,0.799385,0.195689,0.466717,0.468076,0.838665,0.824796,0.929973,0.645691,0.473086,0.63539,0.577288,0.964379,0.429378,0.986926,0.983556,0.281092,0.865711,0.82917,0.0849384,0.994115,0.98168,0.999711,0.963567,0.938847,0.645012,0.999144,0.835164,0.376665,0.968879,0.0755438,0.999581,0.985455,0.681351,0.537924,0.996508,0.929895,0.534619,0.993184,0.992363,0.999505,0.995913,0.895842,0.984037,0.234366,0.895623,0.133852,0.932692,0.970037,0.901543,0.873364,0.174756,0.435792,0.90684,0.976004,0.816698,0.84922,0.913655,0.829036,0.0159768,0.204887,0.916931,0.998772,0.995029,0.806924
}}
}}

Revision as of 14:04, 5 September 2012


Full id: C215_chronic_acute_peripheral_Hepatocyte_osteosarcoma_NK_immature



Phase1 CAGE Peaks

Hg19::chr10:22607676..22607682,+p21@COMMD3
Hg19::chr10:22607725..22607736,+p18@COMMD3
Hg19::chr10:34307354..34307364,+p@chr10:34307354..34307364
+
Hg19::chr12:10084960..10084974,-p1@CLEC2A
Hg19::chr12:10084999..10085009,-p2@CLEC2A
Hg19::chr12:10095845..10095862,-p2@uc001qwo.1
Hg19::chr12:10151709..10151754,-p1@CLEC1B
Hg19::chr12:10151773..10151784,-p3@CLEC1B
Hg19::chr12:10205100..10205121,+p3@AB590792
Hg19::chr12:10205127..10205138,+p5@AB590792
Hg19::chr12:43611998..43612001,+p@chr12:43611998..43612001
+
Hg19::chr12:43612012..43612028,+p@chr12:43612012..43612028
+
Hg19::chr13:73126300..73126304,-p@chr13:73126300..73126304
-
Hg19::chr15:88484080..88484087,-p20@NTRK3
Hg19::chr19:33960599..33960608,-p@chr19:33960599..33960608
-
Hg19::chr19:46663654..46663668,+p@chr19:46663654..46663668
+
Hg19::chr21:20985006..20985010,+p@chr21:20985006..20985010
+
Hg19::chr21:22483836..22483880,+p@chr21:22483836..22483880
+
Hg19::chr21:22550109..22550126,+p@chr21:22550109..22550126
+
Hg19::chr21:22550139..22550141,+p@chr21:22550139..22550141
+
Hg19::chr21:22550147..22550151,+p@chr21:22550147..22550151
+
Hg19::chr21:22550165..22550181,+p@chr21:22550165..22550181
+
Hg19::chr21:47809029..47809044,+p@chr21:47809029..47809044
+
Hg19::chr22:49886217..49886230,-p@chr22:49886217..49886230
-
Hg19::chr22:49886244..49886251,-p@chr22:49886244..49886251
-
Hg19::chr2:164580742..164580760,-p@chr2:164580742..164580760
-
Hg19::chr2:219849008..219849011,-p13@FEV
Hg19::chr2:219849012..219849065,-p1@FEV
Hg19::chr2:219849078..219849085,-p10@FEV
Hg19::chr2:219849175..219849187,-p4@FEV
Hg19::chr2:219849306..219849309,+p@chr2:219849306..219849309
+
Hg19::chr3:126207173..126207218,-p@chr3:126207173..126207218
-
Hg19::chr4:117273886..117273928,+p@chr4:117273886..117273928
+
Hg19::chr4:134283870..134283873,+p@chr4:134283870..134283873
+
Hg19::chr4:42154250..42154256,-p12@BEND4
Hg19::chr4:42154592..42154600,-p15@BEND4
Hg19::chr4:90799994..90800011,+p@chr4:90799994..90800011
+
Hg19::chr5:120355553..120355565,-p@chr5:120355553..120355565
-
Hg19::chr5:155210..155224,+p@chr5:155210..155224
+
Hg19::chr5:155367..155409,+p@chr5:155367..155409
+
Hg19::chr5:155432..155458,+p@chr5:155432..155458
+
Hg19::chr5:86090158..86090169,+p@chr5:86090158..86090169
+
Hg19::chr5:86090206..86090212,+p@chr5:86090206..86090212
+
Hg19::chr5:86213307..86213310,+p@chr5:86213307..86213310
+
Hg19::chr6:135668066..135668095,-p@chr6:135668066..135668095
-
Hg19::chr6:21065386..21065400,+p5@CDKAL1
Hg19::chr6:23916407..23916457,+p@chr6:23916407..23916457
+
Hg19::chr6:67780097..67780102,+p@chr6:67780097..67780102
+
Hg19::chr7:10000571..10000582,+p1@ENST00000451755
Hg19::chr7:10000610..10000618,+p2@ENST00000451755
Hg19::chr7:10000640..10000645,+p4@ENST00000451755
Hg19::chr8:108334188..108334201,-p11@ANGPT1
Hg19::chr8:108334209..108334228,-p8@ANGPT1
Hg19::chr8:108336622..108336625,+p@chr8:108336622..108336625
+
Hg19::chr8:114449751..114449769,-p7@CSMD3
Hg19::chr8:114725643..114725660,-p@chr8:114725643..114725660
-
Hg19::chr8:114747320..114747347,-p@chr8:114747320..114747347
-
Hg19::chr8:114747363..114747380,-p@chr8:114747363..114747380
-
Hg19::chr8:115089397..115089400,+p@chr8:115089397..115089400
+
Hg19::chr8:116673894..116673913,-p12@TRPS1
Hg19::chr8:130648181..130648190,-p@chr8:130648181..130648190
-
Hg19::chr8:2163693..2163732,-p@chr8:2163693..2163732
-
Hg19::chr8:2163883..2163896,-p@chr8:2163883..2163896
-
Hg19::chr8:2163929..2163941,-p@chr8:2163929..2163941
-
Hg19::chr8:41292975..41292985,+p2@ENST00000521725
Hg19::chr8:41292988..41293000,+p1@ENST00000521725
Hg19::chr8:76077242..76077244,+p@chr8:76077242..76077244
+
Hg19::chr9:133407203..133407218,+p@chr9:133407203..133407218
+
Hg19::chr9:133407256..133407273,+p@chr9:133407256..133407273
+


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

No results for this coexpression

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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
adult organism3.17e-15115
neural tube3.84e-0957
neural rod3.84e-0957
future spinal cord3.84e-0957
neural keel3.84e-0957
anterior neural tube9.85e-0842
regional part of forebrain1.66e-0741
forebrain1.66e-0741
future forebrain1.66e-0741
regional part of brain1.99e-0759
regional part of nervous system5.93e-0794
nervous system5.93e-0794
Disease
Ontology termp-valuen
leukemia9.70e-1339
myeloid leukemia8.95e-1231
hematologic cancer7.01e-1151
immune system cancer7.01e-1151


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#promotersEnrichmentp-valueq-value
SUZ12#2351253.631578326888620.01235455260604420.0447305387097916



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

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