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Coexpression cluster:C3776: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.03e-35!115;UBERON:0001049!4.46e-21!57;UBERON:0005068!4.46e-21!57;UBERON:0006241!4.46e-21!57;UBERON:0007135!4.46e-21!57;UBERON:0005743!5.08e-20!86;UBERON:0003075!1.56e-19!86;UBERON:0007284!1.56e-19!86;UBERON:0004111!2.00e-19!241;UBERON:0000025!3.10e-19!194;UBERON:0002616!4.94e-19!59;UBERON:0000477!5.33e-19!286;UBERON:0001017!1.10e-18!82;UBERON:0000073!1.21e-18!94;UBERON:0001016!1.21e-18!94;UBERON:0000955!1.34e-18!69;UBERON:0006238!1.34e-18!69;UBERON:0000483!1.76e-17!309;UBERON:0000119!2.45e-17!312;UBERON:0002346!4.87e-17!90;UBERON:0003080!1.08e-14!42;UBERON:0002780!2.25e-14!41;UBERON:0001890!2.25e-14!41;UBERON:0006240!2.25e-14!41;UBERON:0000033!1.85e-12!123;UBERON:0003056!2.17e-12!61;UBERON:0000468!4.87e-12!659;UBERON:0000153!5.58e-12!129;UBERON:0007811!5.58e-12!129;UBERON:0001893!1.02e-11!34;UBERON:0002020!1.22e-11!34;UBERON:0003528!1.22e-11!34;UBERON:0000467!3.32e-11!625;UBERON:0002791!4.30e-11!33;UBERON:0000475!4.74e-11!365;UBERON:0000481!4.86e-11!347;UBERON:0000480!5.38e-11!626;UBERON:0001869!1.00e-10!32;UBERON:0004121!4.38e-10!169;UBERON:0000924!5.56e-09!173;UBERON:0006601!5.56e-09!173;UBERON:0007100!9.16e-09!27;UBERON:0004872!1.06e-08!84;UBERON:0002619!1.44e-08!22;UBERON:0000062!2.60e-08!511;UBERON:0000922!4.00e-08!612;UBERON:0001950!8.81e-08!20;UBERON:0003076!1.02e-07!15;UBERON:0003057!1.02e-07!15;UBERON:0000956!1.87e-07!25;UBERON:0000203!1.87e-07!25;UBERON:0002050!2.18e-07!605;UBERON:0005423!2.18e-07!605;UBERON:0000923!2.36e-07!604;UBERON:0005291!2.36e-07!604;UBERON:0006598!2.36e-07!604;UBERON:0002532!2.36e-07!604;UBERON:0000948!4.06e-07!24;UBERON:0005498!4.06e-07!24;UBERON:0004140!4.06e-07!24;UBERON:0009881!4.06e-07!24;UBERON:0004141!4.06e-07!24;UBERON:0003084!4.06e-07!24;UBERON:0007005!4.06e-07!24;UBERON:0004139!4.06e-07!24;UBERON:0004291!4.06e-07!24;UBERON:0002049!8.06e-07!79;UBERON:0007798!8.06e-07!79;UBERON:0001009!8.26e-07!113;UBERON:0004732!9.79e-07!13
|ontology_enrichment_uberon=UBERON:0007023!7.03e-35!115;UBERON:0001049!4.46e-21!57;UBERON:0005068!4.46e-21!57;UBERON:0006241!4.46e-21!57;UBERON:0007135!4.46e-21!57;UBERON:0005743!5.08e-20!86;UBERON:0003075!1.56e-19!86;UBERON:0007284!1.56e-19!86;UBERON:0004111!2.00e-19!241;UBERON:0000025!3.10e-19!194;UBERON:0002616!4.94e-19!59;UBERON:0000477!5.33e-19!286;UBERON:0001017!1.10e-18!82;UBERON:0000073!1.21e-18!94;UBERON:0001016!1.21e-18!94;UBERON:0000955!1.34e-18!69;UBERON:0006238!1.34e-18!69;UBERON:0000483!1.76e-17!309;UBERON:0000119!2.45e-17!312;UBERON:0002346!4.87e-17!90;UBERON:0003080!1.08e-14!42;UBERON:0002780!2.25e-14!41;UBERON:0001890!2.25e-14!41;UBERON:0006240!2.25e-14!41;UBERON:0000033!1.85e-12!123;UBERON:0003056!2.17e-12!61;UBERON:0000468!4.87e-12!659;UBERON:0000153!5.58e-12!129;UBERON:0007811!5.58e-12!129;UBERON:0001893!1.02e-11!34;UBERON:0002020!1.22e-11!34;UBERON:0003528!1.22e-11!34;UBERON:0000467!3.32e-11!625;UBERON:0002791!4.30e-11!33;UBERON:0000475!4.74e-11!365;UBERON:0000481!4.86e-11!347;UBERON:0000480!5.38e-11!626;UBERON:0001869!1.00e-10!32;UBERON:0004121!4.38e-10!169;UBERON:0000924!5.56e-09!173;UBERON:0006601!5.56e-09!173;UBERON:0007100!9.16e-09!27;UBERON:0004872!1.06e-08!84;UBERON:0002619!1.44e-08!22;UBERON:0000062!2.60e-08!511;UBERON:0000922!4.00e-08!612;UBERON:0001950!8.81e-08!20;UBERON:0003076!1.02e-07!15;UBERON:0003057!1.02e-07!15;UBERON:0000956!1.87e-07!25;UBERON:0000203!1.87e-07!25;UBERON:0002050!2.18e-07!605;UBERON:0005423!2.18e-07!605;UBERON:0000923!2.36e-07!604;UBERON:0005291!2.36e-07!604;UBERON:0006598!2.36e-07!604;UBERON:0002532!2.36e-07!604;UBERON:0000948!4.06e-07!24;UBERON:0005498!4.06e-07!24;UBERON:0004140!4.06e-07!24;UBERON:0009881!4.06e-07!24;UBERON:0004141!4.06e-07!24;UBERON:0003084!4.06e-07!24;UBERON:0007005!4.06e-07!24;UBERON:0004139!4.06e-07!24;UBERON:0004291!4.06e-07!24;UBERON:0002049!8.06e-07!79;UBERON:0007798!8.06e-07!79;UBERON:0001009!8.26e-07!113;UBERON:0004732!9.79e-07!13
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60149,0.123526,0.0906475,0.0558058,0.0443426,0.00662343,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.26144,0.0286025,1.99608e-06,0.000564671,0.038848,0.00394051,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.0144628,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00128046,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.288159,0.21727,0.289306,0.000310064,0.192475,0.177967,1.33267e-08,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.000919297,3.63782e-14,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.000415994,0.152372,0.0203723,6.14922e-06,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,6.1055e-08,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.000874248,0.0590944,0.247324,0.178389,0.0257622,0.231073,0.0020598,8.08672e-06,0.0360851,0.0021796,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.120472,0.197484,0.396996,0.36145,0.0966095,0.381071,0.057779,0.0863135,0.432035,0.366326,0.390366,0.48809,8.61357e-05,0.443185,0.522904,0.000322406,5.34955e-09,0.227104,0.166658,0.250246,0.38649,0.284625,0.156746,0.55194,0.0437169,0.28907,0.164197,0.0252589,0.287881,0.0556235,0.138768,0.336276,0.468444,0.258219,0.446557,0.243383,0.0659137,0.0140783,0.000456298,0.319063,0.161598,0.000599447,0.0868402,0.496032,0.00613559,0.37357,0.0203982,0.477353,0.00104348,0.000558506,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.000226517,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.194707,0.616388,0.408413,0.516511,0.322213,0.28903,0.33942,0.0700181,0.387276,0.522605,0.481611,0.00800402,0.222037,0.416621,0.416292,0.462712,0.148994,0.215157,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.00357741,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.0980968,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.00977892,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.457886,0.0344603,0.220231,0.159791,0.196976,0.191517,0.463751,0.0145214,0.307334,0.0246928,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.0111711,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.0218443,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0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}}
}}

Revision as of 12:08, 5 September 2012


Full id: C3776_skeletal_occipital_cerebellum_pons_left_postcentral_paracentral



Phase1 CAGE Peaks

Hg19::chr19:35521408..35521423,+p5@SCN1B
Hg19::chr19:35521594..35521614,+p6@SCN1B
Hg19::chr19:35521616..35521647,+p3@SCN1B


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
mesodermal cell1.71e-08119
lining cell3.53e-0757
barrier cell3.53e-0757
Uber Anatomy
Ontology termp-valuen
adult organism7.03e-35115
neural tube4.46e-2157
neural rod4.46e-2157
future spinal cord4.46e-2157
neural keel4.46e-2157
neural plate1.56e-1986
presumptive neural plate1.56e-1986
anatomical conduit2.00e-19241
tube3.10e-19194
regional part of brain4.94e-1959
anatomical cluster5.33e-19286
central nervous system1.10e-1882
regional part of nervous system1.21e-1894
nervous system1.21e-1894
brain1.34e-1869
future brain1.34e-1869
epithelium1.76e-17309
cell layer2.45e-17312
neurectoderm4.87e-1790
anterior neural tube1.08e-1442
regional part of forebrain2.25e-1441
forebrain2.25e-1441
future forebrain2.25e-1441
head1.85e-12123
pre-chordal neural plate2.17e-1261
multi-cellular organism4.87e-12659
anterior region of body5.58e-12129
craniocervical region5.58e-12129
telencephalon1.02e-1134
gray matter1.22e-1134
brain grey matter1.22e-1134
anatomical system3.32e-11625
regional part of telencephalon4.30e-1133
organism subdivision4.74e-11365
multi-tissue structure4.86e-11347
anatomical group5.38e-11626
cerebral hemisphere1.00e-1032
ectoderm-derived structure4.38e-10169
ectoderm5.56e-09173
presumptive ectoderm5.56e-09173
primary circulatory organ9.16e-0927
splanchnic layer of lateral plate mesoderm1.06e-0884
regional part of cerebral cortex1.44e-0822
organ2.60e-08511
embryo4.00e-08612
neocortex8.81e-0820
posterior neural tube1.02e-0715
chordal neural plate1.02e-0715
cerebral cortex1.87e-0725
pallium1.87e-0725
embryonic structure2.18e-07605
developing anatomical structure2.18e-07605
germ layer2.36e-07604
embryonic tissue2.36e-07604
presumptive structure2.36e-07604
epiblast (generic)2.36e-07604
heart4.06e-0724
primitive heart tube4.06e-0724
primary heart field4.06e-0724
anterior lateral plate mesoderm4.06e-0724
heart tube4.06e-0724
heart primordium4.06e-0724
cardiac mesoderm4.06e-0724
cardiogenic plate4.06e-0724
heart rudiment4.06e-0724
vasculature8.06e-0779
vascular system8.06e-0779
circulatory system8.26e-07113
segmental subdivision of nervous system9.79e-0713


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
CCNT2#90536.336201576962630.003930750035764890.0189986858101282
E2F1#186934.907389214879320.008460985347239390.0325316367367498
EGR1#195834.988179094810140.008056488137383440.0320537738887691
FOS#235338.99795530889440.001372499272417130.00897292341233005
FOSL1#8061339.7135797163731.59554825631833e-050.000371047571457649
GABPB1#255337.067683836182170.002832212825417420.015406712603457
JUN#3725312.51282919233630.0005103313992726250.00444154175071947
JUND#372736.994663941871030.002921845042734990.0156738699685757



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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