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Coexpression cluster:C3516: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0007016!cytoskeletal anchoring!0.0203931479008706!50944$GO:0030425!dendrite!0.0351965362914896!50944$GO:0043005!neuron projection!0.0499528239615196!50944
|gostat_on_coexpression_clusters=GO:0007016!cytoskeletal anchoring!0.0203931479008706!50944$GO:0030425!dendrite!0.0351965362914896!50944$GO:0043005!neuron projection!0.0499528239615196!50944
|id=C3516
|id=C3516
|ontology_enrichment_celltype=CL:0000055!5.27e-16!180;CL:0000057!1.30e-07!75;CL:0000393!5.45e-07!60;CL:0000211!5.45e-07!60
|ontology_enrichment_celltype=CL:0002322!2.58e-07!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.56e-28!57;UBERON:0005068!2.56e-28!57;UBERON:0006241!2.56e-28!57;UBERON:0007135!2.56e-28!57;UBERON:0001017!1.80e-27!82;UBERON:0002616!8.88e-26!59;UBERON:0005743!1.56e-25!86;UBERON:0000073!1.77e-25!94;UBERON:0001016!1.77e-25!94;UBERON:0000955!2.74e-23!69;UBERON:0006238!2.74e-23!69;UBERON:0002780!5.11e-23!41;UBERON:0001890!5.11e-23!41;UBERON:0006240!5.11e-23!41;UBERON:0002346!1.00e-22!90;UBERON:0003080!7.42e-22!42;UBERON:0003075!1.91e-20!86;UBERON:0007284!1.91e-20!86;UBERON:0001893!1.51e-19!34;UBERON:0002020!1.82e-19!34;UBERON:0003528!1.82e-19!34;UBERON:0002791!7.76e-19!33;UBERON:0001869!2.08e-18!32;UBERON:0002619!3.08e-15!22;UBERON:0003056!3.04e-14!61;UBERON:0000924!4.08e-14!173;UBERON:0006601!4.08e-14!173;UBERON:0000956!4.81e-14!25;UBERON:0000203!4.81e-14!25;UBERON:0001950!7.50e-14!20;UBERON:0000153!4.60e-13!129;UBERON:0007811!4.60e-13!129;UBERON:0000033!4.76e-13!123;UBERON:0007023!7.25e-13!115;UBERON:0004121!1.55e-12!169;UBERON:0000025!2.30e-12!194;UBERON:0000475!7.88e-10!365;UBERON:0000119!4.84e-09!312;UBERON:0000483!5.35e-09!309;UBERON:0004111!1.67e-08!241;UBERON:0003076!1.27e-07!15;UBERON:0003057!1.27e-07!15;UBERON:0000477!1.34e-07!286;UBERON:0002420!4.22e-07!9;UBERON:0007245!4.22e-07!9;UBERON:0010009!4.22e-07!9;UBERON:0010011!4.22e-07!9;UBERON:0000454!4.22e-07!9;UBERON:0002308!6.24e-07!9;UBERON:0000125!6.24e-07!9
|ontology_enrichment_uberon=UBERON:0001017!1.61e-63!81;UBERON:0001049!8.93e-62!56;UBERON:0005068!8.93e-62!56;UBERON:0006241!8.93e-62!56;UBERON:0007135!8.93e-62!56;UBERON:0001016!9.98e-62!89;UBERON:0000073!1.35e-57!53;UBERON:0002616!1.35e-57!53;UBERON:0000955!1.82e-51!68;UBERON:0006238!1.82e-51!68;UBERON:0002780!7.21e-49!41;UBERON:0001890!7.21e-49!41;UBERON:0003080!7.21e-49!41;UBERON:0006240!7.21e-49!41;UBERON:0002346!3.65e-47!86;UBERON:0007023!1.21e-42!114;UBERON:0001893!2.94e-42!34;UBERON:0003528!3.55e-42!34;UBERON:0002020!3.55e-42!34;UBERON:0003075!3.93e-42!82;UBERON:0007284!3.93e-42!82;UBERON:0001869!1.28e-39!32;UBERON:0002791!3.23e-39!32;UBERON:0002619!2.44e-34!22;UBERON:0003056!5.05e-34!61;UBERON:0004121!2.90e-31!171;UBERON:0000924!2.90e-31!171;UBERON:0006601!2.90e-31!171;UBERON:0001950!4.03e-31!20;UBERON:0010371!6.93e-31!104;UBERON:0000956!1.92e-29!25;UBERON:0000203!1.92e-29!25;UBERON:0011216!7.63e-26!223;UBERON:0010314!2.19e-25!132;UBERON:0000025!4.35e-15!192;UBERON:0002420!1.51e-14!9;UBERON:0007245!1.51e-14!9;UBERON:0010009!1.51e-14!9;UBERON:0010011!1.51e-14!9;UBERON:0000454!1.51e-14!9;UBERON:0000477!3.38e-14!373;UBERON:0000125!3.79e-14!9;UBERON:0002308!3.79e-14!9;UBERON:0003076!1.08e-13!15;UBERON:0003057!1.08e-13!15;UBERON:0009663!2.91e-11!7;UBERON:0004732!3.84e-11!13;UBERON:0000200!4.46e-11!6;UBERON:0004111!2.75e-10!240;UBERON:0002298!4.47e-10!6;UBERON:0004733!5.47e-10!12;UBERON:0002028!5.47e-10!12;UBERON:0007277!5.47e-10!12;UBERON:0000349!9.12e-10!5;UBERON:0001872!1.44e-09!5;UBERON:0001871!1.68e-09!6;UBERON:0002021!4.33e-09!5;UBERON:0000064!5.88e-08!218;UBERON:0001894!6.07e-08!7;UBERON:0006222!6.07e-08!7;UBERON:0000369!1.71e-07!4;UBERON:0002435!1.71e-07!4;UBERON:0000204!1.71e-07!4;UBERON:0010082!1.71e-07!4;UBERON:0002784!3.21e-07!4;UBERON:0000481!4.06e-07!342;UBERON:0000922!8.78e-07!592
|tf_chipseq_enrich=POU5F1#5460;1:111.813067150635:0.00891691105511183:0.0338226655656579
|tf_chipseq_enrich=POU5F1#5460;1:111.813067150635:0.00891691105511183:0.0338226655656579
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052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.190156,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.090504,0.237101,0.0458068,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00128046,0.120459,0.051838,0.00511251,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00049486,0.000122353,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,4.67397e-05,0.000141874,0.206454,0.00206897,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.000748789,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.0058211,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.00213659,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.0161946,0.00318326,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.0455669,0.0210947,0.37006,0.42622,0.120472,0.197484,0.396996,0.36145,0.406019,0.381071,0.216033,0.0210246,0.432035,1.02726e-06,0.390366,0.48809,0.0334527,0.0217093,0.0391928,0.00142909,0.00516504,0.227104,0.518585,0.0734371,0.38649,0.284625,0.00583062,0.0091887,0.00228337,0.28907,0.164197,0.0252589,0.287881,0.21103,0.138768,0.336276,0.132529,0.258219,0.446557,0.243383,5.59455e-07,0.390974,1.07621e-05,2.74091e-05,0.161598,2.12518e-06,0.021206,0.0323708,1.05823e-06,0.37357,8.87042e-08,0.0282154,0.00492096,2.67609e-08,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,1.97791e-05,0.0961477,0.055627,0.354789,0.163828,0.230581,0.120226,0.00486063,0.20075,0.0556238,0.181415,0.282286,0.000180531,0.616388,0.408413,0.165147,0.322213,0.28903,0.33942,0.0700181,0.387276,0.522605,0.0816402,0.000151141,0.222037,0.102227,0.416292,0.462712,1.06909e-05,0.057399,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.056391,0.140384,0.175199,0.0628556,0.0805711,0.170369,0.0980968,0.0768488,0.534741,0.0889149,0.363192,0.236011,0.203486,0.273398,0.0816179,0.4466,0.351067,0.275347,0.269604,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,6.63644e-08,0.250964,0.383276,0.125961,0.504711,0.220231,0.0355483,0.196976,0.191517,0.463751,0.0145214,0.307334,0.459728,0.283463,0.0102434,0.472935,0.399569,0.273281,0.368095,0.275089,0.0858306,0.0283414,0.359231,0.339729,0.197805,0.000423937,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.0260582,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.012591,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.0172483,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.0234202,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.00181011,0.21593,0.158479,0.220319,0.0204324,0.124213,0.259632,0.30793,0.0173907,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.0246892,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.0381402,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.09357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}}
}}

Revision as of 15:10, 19 October 2012


Full id: C3516_neuroectodermal_insula_temporal_amygdala_hippocampus_frontal_postcentral



Phase1 CAGE Peaks

Hg19::chr15:77925296..77925307,-p5@LINGO1
Hg19::chr19:51223018..51223080,-p1@SHANK1
Hg19::chr1:177140052..177140086,+p1@FAM5B


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


GO IDGO nameFDR corrected p-value
GO:0007016cytoskeletal anchoring0.0203931479008706
GO:0030425dendrite0.0351965362914896
GO:0043005neuron projection0.0499528239615196



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
embryonic stem cell2.58e-075
Uber Anatomy
Ontology termp-valuen
central nervous system1.61e-6381
neural tube8.93e-6256
neural rod8.93e-6256
future spinal cord8.93e-6256
neural keel8.93e-6256
nervous system9.98e-6289
regional part of nervous system1.35e-5753
regional part of brain1.35e-5753
brain1.82e-5168
future brain1.82e-5168
regional part of forebrain7.21e-4941
forebrain7.21e-4941
anterior neural tube7.21e-4941
future forebrain7.21e-4941
neurectoderm3.65e-4786
adult organism1.21e-42114
telencephalon2.94e-4234
brain grey matter3.55e-4234
gray matter3.55e-4234
neural plate3.93e-4282
presumptive neural plate3.93e-4282
cerebral hemisphere1.28e-3932
regional part of telencephalon3.23e-3932
regional part of cerebral cortex2.44e-3422
pre-chordal neural plate5.05e-3461
ectoderm-derived structure2.90e-31171
ectoderm2.90e-31171
presumptive ectoderm2.90e-31171
neocortex4.03e-3120
ecto-epithelium6.93e-31104
cerebral cortex1.92e-2925
pallium1.92e-2925
organ system subdivision7.63e-26223
structure with developmental contribution from neural crest2.19e-25132
tube4.35e-15192
basal ganglion1.51e-149
nuclear complex of neuraxis1.51e-149
aggregate regional part of brain1.51e-149
collection of basal ganglia1.51e-149
cerebral subcortex1.51e-149
anatomical cluster3.38e-14373
neural nucleus3.79e-149
nucleus of brain3.79e-149
posterior neural tube1.08e-1315
chordal neural plate1.08e-1315
telencephalic nucleus2.91e-117
segmental subdivision of nervous system3.84e-1113
gyrus4.46e-116
anatomical conduit2.75e-10240
brainstem4.47e-106
segmental subdivision of hindbrain5.47e-1012
hindbrain5.47e-1012
presumptive hindbrain5.47e-1012
limbic system9.12e-105
parietal lobe1.44e-095
temporal lobe1.68e-096
occipital lobe4.33e-095
organ part5.88e-08218
diencephalon6.07e-087
future diencephalon6.07e-087
corpus striatum1.71e-074
striatum1.71e-074
ventral part of telencephalon1.71e-074
future corpus striatum1.71e-074
regional part of diencephalon3.21e-074
multi-tissue structure4.06e-07342
embryo8.78e-07592


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
POU5F1#54601111.8130671506350.008916911055111830.0338226655656579



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.