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Coexpression cluster:C1368: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;5:10.6207764446283:1.66659417606133e-05:0.000384402449544322!REST#5978;5:8.04169059677335:6.54774545315482e-05:0.00106136890793425!SUZ12#23512;5:41.7631507592191:1.86145137032345e-08:1.33522060209623e-06
|tf_chipseq_enrich=GATA2#2624;5:10.6207764446283:1.66659417606133e-05:0.000384402449544322!REST#5978;5:8.04169059677335:6.54774545315482e-05:0.00106136890793425!SUZ12#23512;5:41.7631507592191:1.86145137032345e-08:1.33522060209623e-06
|tfbs_overrepresentation=2.22286e-12,3.9147e-09,0.462362,3.52305e-06,4.69897e-07,0.148479,0.000106054,0.00486477,1.13815e-10,3.05835e-09,7.88034e-07,0.0018909,1.6075e-08,0.000176843,1.9226e-15,0.119969,2.28721e-17,6.10952e-16,0.000196808,5.31804e-09,5.18979e-06,0.000217523,0.157234,4.13868e-16,9.57866e-05,2.66574e-09,5.65705e-15,0.0159512,0.0392706,0.0010848,5.683e-07,0.000118181,0.0357376,0.012009,0.128625,0.161809,0.412076,7.9256e-16,3.69692e-10,0.00869767,6.00861e-05,2.45831e-09,0.000271642,0.334176,0.000149773,0.0711697,2.81961e-10,5.10791e-10,0.0238222,2.89212e-13,2.64906e-05,0.105423,0.135407,0.177342,2.49477e-08,2.23634e-18,9.28833e-05,0.000140377,0.000640432,8.64732e-05,0.0579941,0.000353464,0.205409,0.146128,6.04349e-06,0.000171579,0.000284997,0.000288072,0.164736,0.3062,7.58143e-07,0.130776,4.98293e-08,6.84445e-41,5.57127e-07,0.0339424,2.42344e-06,9.31062e-14,6.89079e-05,0.000104943,3.92611e-31,4.49269e-13,7.43856e-14,3.65459e-15,0.00543919,1.22085e-08,4.87019e-26,0.00138941,4.63208e-06,2.73577e-07,4.49577e-13,0.000162558,5.41807e-11,1.87311e-17,0.163486,0.216824,4.85698e-08,0.28366,1.80435e-14,1.04232e-10,1.44189e-18,5.84791e-05,0.263619,2.45942e-14,1.54083e-10,1.9019e-06,2.99913e-12,2.33501e-07,5.04247e-14,0.131062,4.23214e-06,0.0668385,0.00445412,0.0350582,8.8374e-11,0.0663658,0.0402636,0.00629657,7.74079e-07,3.44902e-08,0.00616773,1.23825e-10,0.00366427,0.164207,7.63412e-05,9.27938e-09,1.50943e-09,0.0293679,3.86268e-13,0.00327222,4.29807e-09,4.8233e-23,3.36154e-09,0.045053,0.235761,8.80268e-14,3.43164e-14,9.09289e-17,4.80871e-05,0.00789487,0.0450332,8.57243e-27,5.47458e-07,0.28766,8.96377e-09,1.41449e-19,9.44194e-08,1.21483e-06,0.0763672,0.0279877,3.09525e-15,1.35584e-20,2.2417e-07,0.0524571,2.25666e-06,1.30155e-25,1.96566e-15,4.68894e-09,0.100724,0.0663128,2.3439e-10,2.27274e-06,0.00211437,1.13124e-06,0.00418962,0.00198872,4.49264e-12,0.0310218,8.76129e-05,0.0010535,0.00772108,0.0361315,4.82916e-05,0.10534,2.57658e-08,3.38532e-11,9.32515e-21,4.1198e-06,3.66451e-06,0.069998,0.292457,0.0024474,3.0956e-13,0.00205682,0.142014,0.00223647,6.43832e-05,4.71806e-14,3.27597e-13,7.8956e-09,1.55147e-07,0.339514,1.28151e-11,0.0962194,0.0244077,0.0919303,4.64634e-17,0.116937,1.43515e-05,0.207318,6.54005e-13,0.00714667,7.94771e-11,0.00719491,2.87487e-08,5.30629e-11,1.75881e-09,2.51386e-15,0.000119726,6.02237e-13,3.0057e-06,5.97007e-21,0.00236917,0.0019174,5.30114e-10,6.32489e-09,3.67651e-05,6.9264e-25,2.79087e-07,2.45625e-12,1.4583e-09,0.000412031,0.00506067,3.32467e-05,2.41944e-17,1.67051e-08,3.26339e-08,0.00084694,2.63453e-20,1.65164e-14,1.11992e-05,8.90206e-07,2.07791e-06,4.76855e-19,5.86912e-05,3.36819e-16,1.81511e-17,2.78927e-07,0.30027,1.17644e-05,2.4075e-07,3.42394e-06,1.60774e-12,0.000764638,1.87866e-13,1.02838e-12,1.65477e-22,0.21083,1.85386e-17,6.47619e-06,5.01237e-12,9.35961e-13,2.55613e-25,2.63896e-09,1.56145e-12,1.83027e-06,3.57931e-12,7.94709e-06,1.69263e-23,0.00904994,0.00750783,4.58577e-16,1.87251e-10,0.0313685,7.56339e-19,2.97603e-05,2.70343e-13,0.0164194,2.82175e-07,0.145331,3.40421e-13,1.15723e-10,0.444637,0.693924,1.0838e-09,0.0746442,0.243403,1.59397e-05,6.84779e-08,0.194104,0.328871,2.86535e-09,3.87312e-06,0.00682278,3.17382e-13,1.26963e-06,0.454695,4.73878e-10,4.47497e-20,0.000121392,0.0124531,0.0478627,5.00802e-12,0.191087,3.23149e-05,2.8722e-14,5.29109e-05,3.6582e-09,3.5966e-23,1.24904e-07,2.31095e-06,1.26133e-13,0.00873599,4.82336e-07,5.16336e-10,0.00098234,4.53021e-12,1.35711e-14,2.70911e-13,6.14876e-15,6.90239e-06,6.47013e-06,4.87525e-08,5.77372e-14,5.78014e-12,5.19934e-05,0.000858981,4.92867e-16,8.7567e-14,1.17596e-21,7.37904e-08,9.97864e-06,6.29194e-10,0.0148408,3.18921e-11,1.12047e-08,0.000635574,1.12836e-13,4.99986e-14,0.00546877,5.66914e-08,0.00842032,2.07138e-06,8.32918e-06,4.83854e-15,3.04479e-11,0.0153332,1.34617e-05,1.35637e-08,2.39763e-07,1.92265e-06,0.0246096,0.000142858,0.0276994,3.53535e-10,0.336852,1.93393e-09,0.00495552,6.3606e-19,7.11818e-06,0.00318529,5.06176e-10,3.33417e-15,0.112682,0.00472567,1.16597e-07,0.00050661,3.02167e-12,1.96031e-05,0.0638804,9.576e-16,2.13037e-06,1.48444e-05,0.00475509,4.17035e-17,6.51789e-06,0.217667,0.00143005,1.31523e-05,4.35831e-19,3.61756e-08,0.0881806,0.000556793,6.94918e-30,5.31028e-08,9.33912e-13,3.05697e-11,7.55316e-07,1.73059e-09,0.726789,4.81423e-08,1.66685e-07,1.56254e-07,0.139162,0.000630352,1.46036e-12,0.0956466,0.000210056,1.15563e-09,1.28558e-13,2.03439e-16,4.6502e-15,7.06822e-05,1.54324e-17,3.11345e-06,0.749103,0.000205151,1.92652e-05,0.269896,0.254659,6.78024e-06,5.42904e-09,0.00171117,0.440842,2.52846e-05,3.19558e-06,1.09222e-09,5.15495e-15,1.51292e-24,0.187452,1.18554e-07,2.43993e-10,1.65284e-10,2.31113e-08,0.000957853,1.16038e-05,1.28397e-09,2.25726e-13,3.6479e-06,0.488244,0.00354074,2.29725e-10,1.63474e-05,1.03962e-10,2.22657e-07,3.61816e-09,8.3141e-07,2.88409e-07,5.94947e-07,3.87926e-06,7.72431e-09,0.109766,4.39138e-06,3.82671e-13,1.07075e-06,5.03207e-07,2.08963e-22,4.0386e-05,6.16915e-09,0.000462337,0.000255538,1.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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,1.23744,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,1.10781,0.574247,0.396295,0.547818,0.530785,0.92701,0.816912,0.225641,0.35719,0.0334022,0.35388,0.585658,6.44584,0.248856,0.936389,0.513952,0.664116,0.390088,0.154075,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,1.61993,0.149032,1.00488,1.15929,0.653901,1.82745,0.62023,0.186533,0.619193,2.22199,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,2.64005,0.483695,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,1.9262,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,1.56093,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,1.48535,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,1.78411,0.378604,0.484017,0.454152,1.27379,2.40891,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1368_neuroblastoma_rectum_small_colon_locus_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chr12:85380546..85380557,+p@chr12:85380546..85380557
+
Hg19::chr4:41750731..41750748,-p1@PHOX2B
Hg19::chr4:41750839..41750850,-p2@PHOX2B
Hg19::chr4:41750860..41750867,-p8@PHOX2B
Hg19::chr4:41750895..41750904,-p6@PHOX2B
Hg19::chr4:41750922..41750939,-p4@PHOX2B


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
sympathetic nervous system4.60e-275
autonomic nervous system4.60e-275
brainstem1.69e-216
intestine4.17e-2117
gastrointestinal system1.07e-1825
locus ceruleus3.98e-172
brainstem nucleus3.98e-172
hindbrain nucleus3.98e-172
peripheral nervous system3.84e-158
small intestine4.23e-154
organ system subdivision4.17e-12223
large intestine6.42e-1211
pons9.83e-123
medulla oblongata1.68e-113
myelencephalon1.68e-113
future myelencephalon1.68e-113
segmental subdivision of hindbrain7.33e-1112
hindbrain7.33e-1112
presumptive hindbrain7.33e-1112
segmental subdivision of nervous system4.88e-1013
mitral valve3.25e-091
vermiform appendix3.53e-091
caecum3.53e-091
midgut3.53e-091
posterior neural tube1.02e-0815
chordal neural plate1.02e-0815
colon1.57e-089
anatomical cluster1.87e-08373
organ segment5.19e-0898
lower digestive tract2.28e-075
nervous system3.00e-0789
Disease
Ontology termp-valuen
neuroendocrine tumor1.34e-226
neuroectodermal tumor1.20e-1310


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
GATA2#2624510.62077644462831.66659417606133e-050.000384402449544322
REST#597858.041690596773356.54774545315482e-050.00106136890793425
SUZ12#23512541.76315075921911.86145137032345e-081.33522060209623e-06



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

This analysis result is provided for C0 - C305 clusters.

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