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Coexpression cluster:C4276: Difference between revisions

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|full_id=C4276_duodenum_occipital_parietal_aorta_temporal_heart_Neural
|full_id=C4276_duodenum_occipital_parietal_aorta_temporal_heart_Neural
|id=C4276
|id=C4276
|ontology_enrichment_celltype=CL:0002139!5.22e-10!24;CL:0000115!3.53e-09!35;CL:0002319!4.69e-08!25;CL:0000071!8.59e-07!18;CL:0002546!8.59e-07!18
|ontology_enrichment_celltype=CL:0002319!2.89e-08!25
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!8.85e-36!94;UBERON:0001016!8.85e-36!94;UBERON:0005743!5.08e-35!86;UBERON:0001017!4.93e-34!82;UBERON:0007023!2.21e-32!115;UBERON:0000955!2.77e-28!69;UBERON:0006238!2.77e-28!69;UBERON:0001049!1.68e-26!57;UBERON:0005068!1.68e-26!57;UBERON:0006241!1.68e-26!57;UBERON:0007135!1.68e-26!57;UBERON:0003075!8.60e-25!86;UBERON:0007284!8.60e-25!86;UBERON:0002346!1.92e-24!90;UBERON:0002616!3.13e-24!59;UBERON:0003080!2.86e-22!42;UBERON:0002780!3.84e-22!41;UBERON:0001890!3.84e-22!41;UBERON:0006240!3.84e-22!41;UBERON:0000924!5.29e-21!173;UBERON:0006601!5.29e-21!173;UBERON:0004121!6.01e-21!169;UBERON:0003056!6.66e-21!61;UBERON:0001893!1.77e-20!34;UBERON:0002020!2.04e-20!34;UBERON:0003528!2.04e-20!34;UBERON:0001869!3.03e-20!32;UBERON:0002791!8.37e-20!33;UBERON:0000033!2.63e-19!123;UBERON:0000153!7.50e-19!129;UBERON:0007811!7.50e-19!129;UBERON:0004111!2.05e-18!241;UBERON:0000025!2.76e-18!194;UBERON:0000468!1.36e-17!659;UBERON:0000477!1.19e-16!286;UBERON:0000956!1.60e-16!25;UBERON:0000203!1.60e-16!25;UBERON:0000483!9.61e-16!309;UBERON:0000119!1.02e-15!312;UBERON:0002619!1.24e-15!22;UBERON:0001950!8.95e-15!20;UBERON:0000475!2.68e-14!365;UBERON:0000467!1.14e-13!625;UBERON:0000480!1.94e-13!626;UBERON:0000922!4.25e-10!612;UBERON:0000064!3.40e-09!219;UBERON:0002050!7.99e-09!605;UBERON:0005423!7.99e-09!605;UBERON:0000923!1.62e-08!604;UBERON:0005291!1.62e-08!604;UBERON:0006598!1.62e-08!604;UBERON:0002532!1.62e-08!604;UBERON:0000481!3.59e-08!347;UBERON:0000062!4.25e-07!511;UBERON:0001986!8.59e-07!18;UBERON:0004638!8.59e-07!18;UBERON:0004852!8.59e-07!18
|ontology_enrichment_uberon=UBERON:0001016!7.65e-37!89;UBERON:0001017!9.58e-37!81;UBERON:0007023!5.52e-33!114;UBERON:0000955!2.62e-30!68;UBERON:0006238!2.62e-30!68;UBERON:0001049!7.32e-28!56;UBERON:0005068!7.32e-28!56;UBERON:0006241!7.32e-28!56;UBERON:0007135!7.32e-28!56;UBERON:0000073!7.63e-27!53;UBERON:0002616!7.63e-27!53;UBERON:0003075!1.63e-26!82;UBERON:0007284!1.63e-26!82;UBERON:0002780!9.49e-25!41;UBERON:0001890!9.49e-25!41;UBERON:0003080!9.49e-25!41;UBERON:0006240!9.49e-25!41;UBERON:0002346!1.13e-24!86;UBERON:0001869!8.40e-24!32;UBERON:0001893!8.84e-24!34;UBERON:0003528!2.26e-23!34;UBERON:0002020!2.26e-23!34;UBERON:0002791!7.42e-23!32;UBERON:0003056!7.48e-23!61;UBERON:0004121!2.69e-20!171;UBERON:0000924!2.69e-20!171;UBERON:0006601!2.69e-20!171;UBERON:0000477!6.85e-20!373;UBERON:0010371!1.08e-19!104;UBERON:0000956!4.51e-19!25;UBERON:0000203!4.51e-19!25;UBERON:0002619!2.24e-18!22;UBERON:0001950!2.89e-17!20;UBERON:0011216!1.19e-16!223;UBERON:0010314!2.39e-15!132;UBERON:0000468!2.07e-14!656;UBERON:0000467!8.94e-13!624;UBERON:0000480!1.29e-12!625;UBERON:0000025!4.37e-12!192;UBERON:0004111!5.21e-12!240;UBERON:0000483!4.44e-10!306;UBERON:0000119!1.38e-09!309;UBERON:0000922!5.81e-08!592;UBERON:0000481!1.59e-07!342;UBERON:0000064!1.98e-07!218;UBERON:0000062!2.30e-07!503;UBERON:0005423!3.03e-07!581;UBERON:0002050!3.42e-07!564;UBERON:0000923!5.15e-07!560;UBERON:0010316!5.15e-07!560;UBERON:0005291!5.15e-07!560;UBERON:0006598!5.15e-07!560;UBERON:0010317!5.15e-07!560;UBERON:0002532!5.15e-07!560
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280380075194233!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017212576020279!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326506373293059!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167908332525533!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666239736505454!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389959826790241
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280380075194233!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017212576020279!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326506373293059!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167908332525533!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666239736505454!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389959826790241
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169234,0.0876426,0.000155001,0.0112557,0.222432,0.107043,0.0043762,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.00490751,0.160149,0.123526,0.0906475,0.00158695,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,3.51254e-05,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.000251928,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.000242011,0.00203513,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.000835367,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,3.77923e-06,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,1.19927e-05,1.02827e-11,0.21727,0.289306,0.119215,0.192475,0.177967,1.93633e-06,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.0505407,0.0713214,0.00224624,0.291114,0.0355833,0.125606,1.87632e-06,0.000216899,1.28372e-06,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,7.46345e-06,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,2.14872e-07,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.170295,0.193653,0.137219,0.0282663,0.251466,0.288096,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.000223227,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.000306535,0.166967,0.188651,0.0813902,0.00122372,0.000720136,0.0546539,0.161789,0.0590944,0.0334734,0.178389,0.000125811,0.231073,0.0161946,8.08672e-06,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.0177337,0.0115948,0.449036,0.407369,0.231447,0.00131394,2.61435e-06,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.057779,0.0863135,0.0198622,2.68462e-16,0.0140037,0.0305485,0.00559336,0.000353311,8.5044e-14,0.875915,2.72893e-07,0.00235168,0.518585,1.04052e-14,0.0135352,0.00488219,0.0344717,2.12137e-05,1.43149e-10,0.28907,0.164197,0.0252589,0.287881,0.21103,0.00445792,1.37386e-08,0.468444,0.258219,3.00528e-06,0.032364,4.14881e-06,0.390974,3.35784e-17,2.23609e-18,0.161598,3.04932e-08,0.644754,0.0323708,1.94637e-09,0.37357,6.9989e-07,0.477353,0.0201095,2.60676e-19,0.0175763,0.20342,0.200493,0.20558,0.00583368,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,5.73524e-09,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.000626841,0.181415,0.282286,8.7005e-09,0.0727621,0.408413,0.165147,0.322213,0.656109,0.33942,0.0700181,0.387276,0.522605,0.0248202,1.56204e-06,0.222037,0.0175112,0.416292,0.128937,1.52985e-11,0.215157,0.204817,0.122646,0.138871,0.027191,0.166905,0.0210039,0.0833851,4.84518e-05,0.140384,0.175199,0.00818864,0.000126574,0.00701509,0.408861,0.365487,0.534741,0.00169836,0.0109626,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,6.55179e-07,0.386538,2.28286e-15,0.250964,0.383276,0.00360665,0.00582796,0.220231,0.159791,0.196976,0.191517,0.00383709,0.235208,0.307334,0.459728,0.283463,2.59931e-05,0.472935,0.399569,0.273281,0.0780405,0.0418805,0.384593,0.138622,0.359231,0.339729,0.197805,0.000423937,0.0870376,0.332774,0.52832,0.299887,1.07042e-05,0.205413,0.17639,0.0779009,0.276869,0.00170381,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.0269454,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.00282612,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.00206803,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,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}}
}}

Revision as of 15:48, 19 October 2012


Full id: C4276_duodenum_occipital_parietal_aorta_temporal_heart_Neural



Phase1 CAGE Peaks

Hg19::chr3:123752181..123752201,+p5@KALRN
Hg19::chr3:123752204..123752234,+p2@KALRN
Hg19::chr3:123752240..123752247,+p15@KALRN


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><br>

Cell Type
Ontology termp-valuen
neural cell2.89e-0825
Uber Anatomy
Ontology termp-valuen
nervous system7.65e-3789
central nervous system9.58e-3781
adult organism5.52e-33114
brain2.62e-3068
future brain2.62e-3068
neural tube7.32e-2856
neural rod7.32e-2856
future spinal cord7.32e-2856
neural keel7.32e-2856
regional part of nervous system7.63e-2753
regional part of brain7.63e-2753
neural plate1.63e-2682
presumptive neural plate1.63e-2682
regional part of forebrain9.49e-2541
forebrain9.49e-2541
anterior neural tube9.49e-2541
future forebrain9.49e-2541
neurectoderm1.13e-2486
cerebral hemisphere8.40e-2432
telencephalon8.84e-2434
brain grey matter2.26e-2334
gray matter2.26e-2334
regional part of telencephalon7.42e-2332
pre-chordal neural plate7.48e-2361
ectoderm-derived structure2.69e-20171
ectoderm2.69e-20171
presumptive ectoderm2.69e-20171
anatomical cluster6.85e-20373
ecto-epithelium1.08e-19104
cerebral cortex4.51e-1925
pallium4.51e-1925
regional part of cerebral cortex2.24e-1822
neocortex2.89e-1720
organ system subdivision1.19e-16223
structure with developmental contribution from neural crest2.39e-15132
multi-cellular organism2.07e-14656
anatomical system8.94e-13624
anatomical group1.29e-12625
tube4.37e-12192
anatomical conduit5.21e-12240
epithelium4.44e-10306
cell layer1.38e-09309
embryo5.81e-08592
multi-tissue structure1.59e-07342
organ part1.98e-07218
organ2.30e-07503
developing anatomical structure3.03e-07581
embryonic structure3.42e-07564
germ layer5.15e-07560
germ layer / neural crest5.15e-07560
embryonic tissue5.15e-07560
presumptive structure5.15e-07560
germ layer / neural crest derived structure5.15e-07560
epiblast (generic)5.15e-07560


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
CTCF#1066435.360256373075030.0064925092527670.0280380075194233
CTCFL#140690319.74647435897440.0001298372005551160.0017212576020279
E2F1#186934.907389214879320.008460985347239390.0326506373293059
EP300#203336.77394172622320.003216880500103790.0167908332525533
RAD21#5885310.35503389545630.0009004912073565420.00666239736505454
ZNF143#7702313.50087655222790.0004062804962997170.00389959826790241



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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