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Coexpression cluster:C3776: Difference between revisions

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|full_id=C3776_skeletal_occipital_cerebellum_pons_left_postcentral_paracentral
|full_id=C3776_skeletal_occipital_cerebellum_pons_left_postcentral_paracentral
|id=C3776
|id=C3776
|ontology_enrichment_celltype=CL:0000222!1.71e-08!119;CL:0000213!3.53e-07!57;CL:0000215!3.53e-07!57
|ontology_enrichment_celltype=
|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!3.18e-34!114;UBERON:0010314!6.88e-29!132;UBERON:0001049!2.00e-26!56;UBERON:0005068!2.00e-26!56;UBERON:0006241!2.00e-26!56;UBERON:0007135!2.00e-26!56;UBERON:0000073!8.34e-25!53;UBERON:0002616!8.34e-25!53;UBERON:0003075!2.02e-24!82;UBERON:0007284!2.02e-24!82;UBERON:0001017!2.13e-23!81;UBERON:0000955!4.67e-23!68;UBERON:0006238!4.67e-23!68;UBERON:0002346!4.82e-22!86;UBERON:0001016!8.47e-21!89;UBERON:0002780!2.59e-18!41;UBERON:0001890!2.59e-18!41;UBERON:0003080!2.59e-18!41;UBERON:0006240!2.59e-18!41;UBERON:0000025!4.71e-18!192;UBERON:0004111!7.57e-18!240;UBERON:0000477!3.21e-17!373;UBERON:0001893!2.21e-16!34;UBERON:0003528!2.25e-16!34;UBERON:0002020!2.25e-16!34;UBERON:0010371!2.56e-16!104;UBERON:0000483!2.73e-16!306;UBERON:0000119!5.60e-16!309;UBERON:0001869!3.32e-15!32;UBERON:0003056!3.56e-15!61;UBERON:0002791!5.52e-15!32;UBERON:0000481!7.57e-12!342;UBERON:0002619!1.20e-11!22;UBERON:0004121!3.70e-11!171;UBERON:0000924!3.70e-11!171;UBERON:0006601!3.70e-11!171;UBERON:0000956!6.29e-11!25;UBERON:0000203!6.29e-11!25;UBERON:0001950!1.41e-10!20;UBERON:0000468!3.24e-10!656;UBERON:0000467!1.24e-09!624;UBERON:0011216!1.55e-09!223;UBERON:0000480!1.67e-09!625;UBERON:0003076!2.32e-09!15;UBERON:0003057!2.32e-09!15;UBERON:0007100!5.17e-09!27;UBERON:0004732!1.26e-08!13;UBERON:0000062!3.61e-08!503;UBERON:0004733!7.83e-08!12;UBERON:0002028!7.83e-08!12;UBERON:0007277!7.83e-08!12;UBERON:0000948!3.37e-07!24;UBERON:0005498!3.37e-07!24;UBERON:0004140!3.37e-07!24;UBERON:0009881!3.37e-07!24;UBERON:0004141!3.37e-07!24;UBERON:0003084!3.37e-07!24;UBERON:0007005!3.37e-07!24;UBERON:0004139!3.37e-07!24;UBERON:0004291!3.37e-07!24;UBERON:0000125!3.61e-07!9;UBERON:0002308!3.61e-07!9;UBERON:0000923!5.36e-07!560;UBERON:0010316!5.36e-07!560;UBERON:0005291!5.36e-07!560;UBERON:0006598!5.36e-07!560;UBERON:0010317!5.36e-07!560;UBERON:0002532!5.36e-07!560;UBERON:0002420!8.82e-07!9;UBERON:0007245!8.82e-07!9;UBERON:0010009!8.82e-07!9;UBERON:0010011!8.82e-07!9;UBERON:0000454!8.82e-07!9
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189986858101282!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325316367367498!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320537738887691!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897292341233005!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371047571457649!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015406712603457!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444154175071947!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156738699685757
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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 15:24, 19 October 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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.18e-34114
structure with developmental contribution from neural crest6.88e-29132
neural tube2.00e-2656
neural rod2.00e-2656
future spinal cord2.00e-2656
neural keel2.00e-2656
regional part of nervous system8.34e-2553
regional part of brain8.34e-2553
neural plate2.02e-2482
presumptive neural plate2.02e-2482
central nervous system2.13e-2381
brain4.67e-2368
future brain4.67e-2368
neurectoderm4.82e-2286
nervous system8.47e-2189
regional part of forebrain2.59e-1841
forebrain2.59e-1841
anterior neural tube2.59e-1841
future forebrain2.59e-1841
tube4.71e-18192
anatomical conduit7.57e-18240
anatomical cluster3.21e-17373
telencephalon2.21e-1634
brain grey matter2.25e-1634
gray matter2.25e-1634
ecto-epithelium2.56e-16104
epithelium2.73e-16306
cell layer5.60e-16309
cerebral hemisphere3.32e-1532
pre-chordal neural plate3.56e-1561
regional part of telencephalon5.52e-1532
multi-tissue structure7.57e-12342
regional part of cerebral cortex1.20e-1122
ectoderm-derived structure3.70e-11171
ectoderm3.70e-11171
presumptive ectoderm3.70e-11171
cerebral cortex6.29e-1125
pallium6.29e-1125
neocortex1.41e-1020
multi-cellular organism3.24e-10656
anatomical system1.24e-09624
organ system subdivision1.55e-09223
anatomical group1.67e-09625
posterior neural tube2.32e-0915
chordal neural plate2.32e-0915
primary circulatory organ5.17e-0927
segmental subdivision of nervous system1.26e-0813
organ3.61e-08503
segmental subdivision of hindbrain7.83e-0812
hindbrain7.83e-0812
presumptive hindbrain7.83e-0812
heart3.37e-0724
primitive heart tube3.37e-0724
primary heart field3.37e-0724
anterior lateral plate mesoderm3.37e-0724
heart tube3.37e-0724
heart primordium3.37e-0724
cardiac mesoderm3.37e-0724
cardiogenic plate3.37e-0724
heart rudiment3.37e-0724
neural nucleus3.61e-079
nucleus of brain3.61e-079
germ layer5.36e-07560
germ layer / neural crest5.36e-07560
embryonic tissue5.36e-07560
presumptive structure5.36e-07560
germ layer / neural crest derived structure5.36e-07560
epiblast (generic)5.36e-07560
basal ganglion8.82e-079
nuclear complex of neuraxis8.82e-079
aggregate regional part of brain8.82e-079
collection of basal ganglia8.82e-079
cerebral subcortex8.82e-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
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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