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Coexpression cluster:C3408: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.39e-41!94;UBERON:0001016!1.39e-41!94;UBERON:0005743!2.09e-41!86;UBERON:0001017!8.87e-40!82;UBERON:0002346!1.38e-37!90;UBERON:0003075!1.58e-35!86;UBERON:0007284!1.58e-35!86;UBERON:0001049!3.30e-33!57;UBERON:0005068!3.30e-33!57;UBERON:0006241!3.30e-33!57;UBERON:0007135!3.30e-33!57;UBERON:0000955!4.41e-33!69;UBERON:0006238!4.41e-33!69;UBERON:0000924!6.64e-32!173;UBERON:0006601!6.64e-32!173;UBERON:0002616!9.73e-32!59;UBERON:0004121!5.01e-30!169;UBERON:0007023!5.89e-29!115;UBERON:0000033!8.06e-27!123;UBERON:0003056!1.09e-26!61;UBERON:0000153!1.10e-26!129;UBERON:0007811!1.10e-26!129;UBERON:0003080!2.32e-24!42;UBERON:0002780!3.94e-24!41;UBERON:0001890!3.94e-24!41;UBERON:0006240!3.94e-24!41;UBERON:0000481!1.18e-23!347;UBERON:0002020!4.12e-20!34;UBERON:0003528!4.12e-20!34;UBERON:0001893!8.02e-20!34;UBERON:0000119!8.24e-20!312;UBERON:0000475!1.08e-19!365;UBERON:0002791!2.45e-19!33;UBERON:0000483!4.10e-19!309;UBERON:0001869!9.20e-19!32;UBERON:0000025!2.38e-15!194;UBERON:0000477!4.10e-15!286;UBERON:0004111!8.67e-15!241;UBERON:0000956!1.13e-14!25;UBERON:0000203!1.13e-14!25;UBERON:0002619!5.03e-14!22;UBERON:0001950!6.85e-13!20;UBERON:0000064!8.53e-11!219;UBERON:0000922!2.23e-10!612;UBERON:0003076!6.93e-10!15;UBERON:0003057!6.93e-10!15;UBERON:0004732!1.54e-08!13;UBERON:0002050!2.55e-08!605;UBERON:0005423!2.55e-08!605;UBERON:0004733!4.00e-08!12;UBERON:0002028!4.00e-08!12;UBERON:0007277!4.00e-08!12;UBERON:0000923!4.60e-08!604;UBERON:0005291!4.60e-08!604;UBERON:0006598!4.60e-08!604;UBERON:0002532!4.60e-08!604;UBERON:0000468!8.65e-08!659;UBERON:0003103!3.79e-07!69;UBERON:0002308!6.30e-07!9;UBERON:0000125!6.30e-07!9
|ontology_enrichment_uberon=UBERON:0000073!1.39e-41!94;UBERON:0001016!1.39e-41!94;UBERON:0005743!2.09e-41!86;UBERON:0001017!8.87e-40!82;UBERON:0002346!1.38e-37!90;UBERON:0003075!1.58e-35!86;UBERON:0007284!1.58e-35!86;UBERON:0001049!3.30e-33!57;UBERON:0005068!3.30e-33!57;UBERON:0006241!3.30e-33!57;UBERON:0007135!3.30e-33!57;UBERON:0000955!4.41e-33!69;UBERON:0006238!4.41e-33!69;UBERON:0000924!6.64e-32!173;UBERON:0006601!6.64e-32!173;UBERON:0002616!9.73e-32!59;UBERON:0004121!5.01e-30!169;UBERON:0007023!5.89e-29!115;UBERON:0000033!8.06e-27!123;UBERON:0003056!1.09e-26!61;UBERON:0000153!1.10e-26!129;UBERON:0007811!1.10e-26!129;UBERON:0003080!2.32e-24!42;UBERON:0002780!3.94e-24!41;UBERON:0001890!3.94e-24!41;UBERON:0006240!3.94e-24!41;UBERON:0000481!1.18e-23!347;UBERON:0002020!4.12e-20!34;UBERON:0003528!4.12e-20!34;UBERON:0001893!8.02e-20!34;UBERON:0000119!8.24e-20!312;UBERON:0000475!1.08e-19!365;UBERON:0002791!2.45e-19!33;UBERON:0000483!4.10e-19!309;UBERON:0001869!9.20e-19!32;UBERON:0000025!2.38e-15!194;UBERON:0000477!4.10e-15!286;UBERON:0004111!8.67e-15!241;UBERON:0000956!1.13e-14!25;UBERON:0000203!1.13e-14!25;UBERON:0002619!5.03e-14!22;UBERON:0001950!6.85e-13!20;UBERON:0000064!8.53e-11!219;UBERON:0000922!2.23e-10!612;UBERON:0003076!6.93e-10!15;UBERON:0003057!6.93e-10!15;UBERON:0004732!1.54e-08!13;UBERON:0002050!2.55e-08!605;UBERON:0005423!2.55e-08!605;UBERON:0004733!4.00e-08!12;UBERON:0002028!4.00e-08!12;UBERON:0007277!4.00e-08!12;UBERON:0000923!4.60e-08!604;UBERON:0005291!4.60e-08!604;UBERON:0006598!4.60e-08!604;UBERON:0002532!4.60e-08!604;UBERON:0000468!8.65e-08!659;UBERON:0003103!3.79e-07!69;UBERON:0002308!6.30e-07!9;UBERON:0000125!6.30e-07!9
|tf_chipseq_enrich=BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138495731920624!CTBP2#1488;2:41.8113335595521:0.000754340825991485:0.00593376527270654!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321207453625705!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319685244901288!GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189426395649597!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156401298968889!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245887012854144!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628487971055167!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328544814207018!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139829331590944!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109118037366963
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237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.0217163,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.090504,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,3.77923e-06,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,8.15339e-05,0.000122353,0.21727,0.289306,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.392974,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.0472142,0.0355833,0.125606,0.175094,4.63445e-08,0.000141874,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.00166615,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.000306535,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.0334734,0.178389,0.0257622,0.231073,0.407281,0.00318326,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,3.35515e-08,0.449036,0.407369,0.231447,0.00858901,0.43956,0.0789454,0.10748,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.580441,0.000699353,0.11074,1.18342e-07,0.390366,0.48809,0.153829,0.00308025,0.522904,6.58045e-05,0.151996,0.227104,0.518585,8.20972e-07,0.38649,0.284625,0.504757,0.0091887,1.22274e-06,0.28907,0.164197,0.462688,0.287881,0.21103,0.138768,0.00846715,0.00403041,0.258219,0.119142,0.243383,8.44761e-10,0.390974,1.84416e-08,0.00120937,0.161598,3.23575e-09,0.021206,0.0323708,1.71167e-08,0.0805771,1.13245e-09,0.138234,0.0201095,2.35949e-07,2.48085e-05,0.20342,0.200493,0.20558,0.300504,0.25656,0.107337,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0101317,0.314429,0.181415,0.282286,4.44343e-06,0.616388,0.408413,0.0374737,0.322213,0.0931134,0.33942,0.243065,0.387276,0.522605,0.0248202,0.00120002,0.222037,0.416621,0.416292,0.462712,0.00246111,0.057399,0.0225745,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,0.0628556,0.373557,0.523625,0.408861,0.0111982,0.178743,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.00388821,0.000553931,0.241132,0.371414,0.0527347,0.303709,0.0323359,0.386538,0.00602464,0.0345164,0.383276,0.125961,0.156714,0.220231,9.82679e-05,0.196976,0.191517,0.463751,0.0145214,0.307334,0.459728,0.283463,0.563586,0.472935,0.0932845,0.273281,0.368095,0.275089,0.384593,0.00444763,0.359231,0.339729,0.197805,1.92631e-12,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.00221755,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.00449563,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.0701861,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.00801612,0.0181384,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.0232077,0.141867,0.193031,0.249101,0.000284685,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.0136582,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.16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}}
}}

Revision as of 13:02, 5 September 2012


Full id: C3408_cerebellum_pineal_rhabdomyosarcoma_neuroectodermal_brain_Pericytes_iPS



Phase1 CAGE Peaks

Hg19::chr14:21994337..21994442,-p1@SALL2
Hg19::chr14:21994449..21994524,-p2@SALL2
Hg19::chr19:49149553..49149602,-p4@CA11


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
neurectodermal cell4.31e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.39e-4194
nervous system1.39e-4194
central nervous system8.87e-4082
neurectoderm1.38e-3790
neural plate1.58e-3586
presumptive neural plate1.58e-3586
neural tube3.30e-3357
neural rod3.30e-3357
future spinal cord3.30e-3357
neural keel3.30e-3357
brain4.41e-3369
future brain4.41e-3369
ectoderm6.64e-32173
presumptive ectoderm6.64e-32173
regional part of brain9.73e-3259
ectoderm-derived structure5.01e-30169
adult organism5.89e-29115
head8.06e-27123
pre-chordal neural plate1.09e-2661
anterior region of body1.10e-26129
craniocervical region1.10e-26129
anterior neural tube2.32e-2442
regional part of forebrain3.94e-2441
forebrain3.94e-2441
future forebrain3.94e-2441
multi-tissue structure1.18e-23347
gray matter4.12e-2034
brain grey matter4.12e-2034
telencephalon8.02e-2034
cell layer8.24e-20312
organism subdivision1.08e-19365
regional part of telencephalon2.45e-1933
epithelium4.10e-19309
cerebral hemisphere9.20e-1932
tube2.38e-15194
anatomical cluster4.10e-15286
anatomical conduit8.67e-15241
cerebral cortex1.13e-1425
pallium1.13e-1425
regional part of cerebral cortex5.03e-1422
neocortex6.85e-1320
organ part8.53e-11219
embryo2.23e-10612
posterior neural tube6.93e-1015
chordal neural plate6.93e-1015
segmental subdivision of nervous system1.54e-0813
embryonic structure2.55e-08605
developing anatomical structure2.55e-08605
segmental subdivision of hindbrain4.00e-0812
hindbrain4.00e-0812
presumptive hindbrain4.00e-0812
germ layer4.60e-08604
embryonic tissue4.60e-08604
presumptive structure4.60e-08604
epiblast (generic)4.60e-08604
multi-cellular organism8.65e-08659
compound organ3.79e-0769
nucleus of brain6.30e-079
neural nucleus6.30e-079


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
BCL3#602223.03140186915890.002464674760842910.0138495731920624
CTBP2#1488241.81133355955210.0007543408259914850.00593376527270654
E2F6#187635.017155731697390.00791769806886330.0321207453625705
EGR1#195834.988179094810140.008056488137383440.0319685244901288
GATA3#2625218.15767757147070.003944546819279620.0189426395649597
JUND#372736.994663941871030.002921845042734990.0156401298968889
SP1#666735.69838137814090.005403962701712170.0245887012854144
TCF12#6938310.63446490218640.0008313523990202070.00628487971055167
YY1#752834.911170749853860.008441455341808260.0328544814207018
ZBTB7A#5134137.35190930787590.002516255860282270.0139829331590944
ZNF263#1012738.221841637010680.001799043925565870.0109118037366963



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.