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Coexpression cluster:C3749: Difference between revisions

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|full_id=C3749_brain_Neurons_parietal_occipital_temporal_cerebellum_medial
|full_id=C3749_brain_Neurons_parietal_occipital_temporal_cerebellum_medial
|id=C3749
|id=C3749
|ontology_enrichment_celltype=CL:0002319!3.63e-11!25;CL:0000047!1.11e-09!8;CL:0000540!4.48e-07!6;CL:0000031!4.48e-07!6;CL:0000404!4.48e-07!6;CL:0000133!9.05e-07!59
|ontology_enrichment_celltype=CL:0000242!2.72e-07!2
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:5409!9.98e-07!4
|ontology_enrichment_uberon=UBERON:0001017!2.70e-78!82;UBERON:0000073!1.90e-76!94;UBERON:0001016!1.90e-76!94;UBERON:0005743!5.03e-76!86;UBERON:0001049!1.26e-74!57;UBERON:0005068!1.26e-74!57;UBERON:0006241!1.26e-74!57;UBERON:0007135!1.26e-74!57;UBERON:0000955!1.40e-64!69;UBERON:0006238!1.40e-64!69;UBERON:0002616!1.72e-62!59;UBERON:0002780!1.74e-59!41;UBERON:0001890!1.74e-59!41;UBERON:0006240!1.74e-59!41;UBERON:0003080!9.26e-58!42;UBERON:0002346!1.65e-55!90;UBERON:0003075!5.47e-53!86;UBERON:0007284!5.47e-53!86;UBERON:0002020!9.99e-50!34;UBERON:0003528!9.99e-50!34;UBERON:0001893!1.40e-49!34;UBERON:0002791!2.93e-48!33;UBERON:0001869!2.94e-46!32;UBERON:0003056!9.86e-42!61;UBERON:0000924!1.06e-41!173;UBERON:0006601!1.06e-41!173;UBERON:0004121!2.23e-39!169;UBERON:0000956!5.41e-36!25;UBERON:0000203!5.41e-36!25;UBERON:0002619!1.65e-32!22;UBERON:0000033!2.02e-32!123;UBERON:0000153!4.66e-30!129;UBERON:0007811!4.66e-30!129;UBERON:0001950!1.21e-29!20;UBERON:0007023!6.93e-27!115;UBERON:0003076!3.22e-17!15;UBERON:0003057!3.22e-17!15;UBERON:0002308!5.82e-15!9;UBERON:0000125!5.82e-15!9;UBERON:0002420!6.52e-15!9;UBERON:0007245!6.52e-15!9;UBERON:0010009!6.52e-15!9;UBERON:0010011!6.52e-15!9;UBERON:0000454!6.52e-15!9;UBERON:0000025!8.05e-15!194;UBERON:0004732!4.02e-14!13;UBERON:0004733!6.86e-13!12;UBERON:0002028!6.86e-13!12;UBERON:0007277!6.86e-13!12;UBERON:0009663!5.56e-12!7;UBERON:0000475!2.20e-11!365;UBERON:0001894!4.84e-11!7;UBERON:0006222!4.84e-11!7;UBERON:0000200!1.38e-10!6;UBERON:0001871!1.74e-10!7;UBERON:0002298!2.74e-10!8;UBERON:0004111!8.99e-10!241;UBERON:0000064!1.45e-09!219;UBERON:0002021!3.16e-09!5;UBERON:0001872!5.45e-09!5;UBERON:0002680!1.06e-08!9;UBERON:0001895!1.06e-08!9;UBERON:0010092!1.06e-08!9;UBERON:0000349!1.17e-08!5;UBERON:0000483!1.25e-07!309;UBERON:0000922!1.35e-07!612;UBERON:0000369!1.91e-07!4;UBERON:0002435!1.91e-07!4;UBERON:0000204!1.91e-07!4;UBERON:0010082!1.91e-07!4;UBERON:0000119!2.13e-07!312;UBERON:0000477!4.00e-07!286;UBERON:0000468!4.23e-07!659
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4,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.00490751,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,4.97064e-05,0.211746,0.220538,9.12913e-05,0.0757897,0.013859,0.193215,0.0549034,0.00312202,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.0154037,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.00782667,0.00615421,0.11002,0.0376172,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.00344747,0.182701,0.0637246,0.147698,0.0105143,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.0306206,0.00327218,0.00136743,0.00511251,0.00127324,4.13072e-05,0.0755121,3.60125e-06,0.144075,0.000585365,0.0741807,0.277091,0.047822,0.655293,0.0255266,0.289306,0.119215,0.192475,0.177967,0.547859,0.00168996,0.047591,0.392974,0.00189135,0.175319,0.300597,0.0713214,0.00224624,0.291114,0.0355833,0.125606,0.0163112,0.0370461,0.145116,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.0004316,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.060512,0.0159074,0.340936,0.151597,6.9439e-07,0.00136247,0.148574,0.504592,0.155821,6.54495e-05,0.0919008,0.0602373,0.000561466,0.15063,0.0973823,0.15503,0.0154015,0.00141547,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.0186145,0.174776,0.0948451,0.0384217,0.0339656,0.140533,0.00515192,0.0364628,0.00020131,0.00664782,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,0.00122372,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,8.04897e-06,0.0998546,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.120614,0.407369,0.000162249,0.18653,0.115047,0.0789454,0.10748,0.022688,0.197484,0.396996,0.36145,0.0160226,0.381071,0.057779,0.276075,0.00272579,0.366326,0.390366,0.0305485,0.0334527,0.00308025,0.522904,0.00142909,0.336835,7.63295e-06,0.00667974,0.617852,0.0867545,0.284625,0.0344717,0.55194,0.144318,0.28907,0.164197,0.00379441,0.287881,0.21103,0.138768,0.0642229,0.468444,0.258219,0.446557,0.032364,0.0186777,0.0889613,0.0115792,0.319063,0.161598,0.013901,0.00422412,0.0323708,0.00613559,0.37357,0.0203982,0.477353,0.000195013,0.160298,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.00960524,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0101317,0.314429,0.0175523,0.282286,0.0192486,0.0727621,0.408413,0.516511,0.322213,0.0931134,0.33942,0.243065,0.387276,0.522605,0.0248202,0.537348,0.0267088,0.416621,0.416292,0.0252635,0.734551,0.0019893,0.204817,0.452428,0.00049814,0.103502,0.166905,0.19783,0.0833851,0.056391,0.00457272,0.175199,0.0628556,0.0805711,0.170369,0.408861,0.365487,0.00780726,0.0889149,0.363192,0.236011,0.203486,0.00428131,0.375787,0.00319628,0.351067,0.00438156,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.00213139,0.0355483,0.196976,0.191517,0.129584,0.00258603,0.307334,0.127092,0.0048173,0.201728,0.472935,0.399569,0.00427533,0.0780405,0.0418805,0.0858306,0.47795,0.359231,0.00876091,0.197805,0.00278185,0.0870376,0.332774,0.00734059,0.000506965,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.0140817,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.00329437,0.378361,0.0358457,0.20753,0.447185,0.0171537,0.193601,0.0264253,0.222977,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.0213665,0.0325925,0.0933115,0.12405,0.179889,0.0279371,0.0430576,0.0855609,0.131118,0.20837,0.247588,0.0267847,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.0701861,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.000267844,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.0183464,0.0026812,0.0367308,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.0215816,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.00208455,0.104603,8.74929e-07,0.00298405,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.0280973,0.29837,0.253509,0.177664,0.28365,0.000290199,0.00908908,0.160658,0.206239,0.19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}}
}}

Revision as of 15:22, 19 October 2012


Full id: C3749_brain_Neurons_parietal_occipital_temporal_cerebellum_medial



Phase1 CAGE Peaks

Hg19::chr19:11562404..11562424,-p@chr19:11562404..11562424
-
Hg19::chr2:27170763..27170781,+p5@DPYSL5
Hg19::chr8:80577410..80577417,+p@chr8:80577410..80577417
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
Merkel cell2.72e-072
Uber Anatomy
Ontology termp-valuen
neural tube2.03e-7756
neural rod2.03e-7756
future spinal cord2.03e-7756
neural keel2.03e-7756
central nervous system1.82e-7581
nervous system4.09e-7389
regional part of nervous system1.63e-6953
regional part of brain1.63e-6953
brain1.31e-6468
future brain1.31e-6468
neurectoderm7.87e-5886
neural plate2.09e-5582
presumptive neural plate2.09e-5582
regional part of forebrain9.65e-5541
forebrain9.65e-5541
anterior neural tube9.65e-5541
future forebrain9.65e-5541
brain grey matter3.30e-5334
gray matter3.30e-5334
telencephalon5.64e-5334
regional part of telencephalon7.43e-4832
cerebral hemisphere2.21e-4732
ecto-epithelium2.83e-46104
ectoderm-derived structure2.65e-41171
ectoderm2.65e-41171
presumptive ectoderm2.65e-41171
pre-chordal neural plate8.25e-4061
regional part of cerebral cortex6.10e-3922
neocortex1.51e-3820
cerebral cortex7.00e-3425
pallium7.00e-3425
structure with developmental contribution from neural crest3.41e-32132
adult organism6.00e-31114
organ system subdivision6.06e-30223
posterior neural tube8.64e-2315
chordal neural plate8.64e-2315
neural nucleus2.42e-219
nucleus of brain2.42e-219
tube1.26e-18192
brainstem5.04e-186
gyrus7.01e-186
basal ganglion2.52e-169
nuclear complex of neuraxis2.52e-169
aggregate regional part of brain2.52e-169
collection of basal ganglia2.52e-169
cerebral subcortex2.52e-169
telencephalic nucleus8.54e-167
segmental subdivision of hindbrain2.46e-1512
hindbrain2.46e-1512
presumptive hindbrain2.46e-1512
segmental subdivision of nervous system4.81e-1413
anatomical cluster1.57e-13373
anatomical conduit8.52e-13240
organ part3.41e-11218
temporal lobe3.64e-116
epithelium1.33e-10306
cell layer2.15e-10309
occipital lobe2.59e-105
parietal lobe3.54e-105
spinal cord5.74e-103
dorsal region element5.74e-103
dorsum5.74e-103
medulla oblongata5.92e-103
myelencephalon5.92e-103
future myelencephalon5.92e-103
pons8.79e-103
frontal cortex9.91e-103
regional part of metencephalon1.90e-089
metencephalon1.90e-089
future metencephalon1.90e-089
embryo8.22e-08592
dorsal plus ventral thalamus1.16e-072
thalamic complex1.16e-072
corpus striatum1.38e-074
striatum1.38e-074
ventral part of telencephalon1.38e-074
future corpus striatum1.38e-074
locus ceruleus2.40e-072
brainstem nucleus2.40e-072
hindbrain nucleus2.40e-072
germ layer2.78e-07560
germ layer / neural crest2.78e-07560
embryonic tissue2.78e-07560
presumptive structure2.78e-07560
germ layer / neural crest derived structure2.78e-07560
epiblast (generic)2.78e-07560
middle temporal gyrus2.80e-072
middle frontal gyrus2.98e-072
globus pallidus3.48e-072
pallidum3.48e-072
embryonic structure3.92e-07564
multi-tissue structure4.83e-07342
Disease
Ontology termp-valuen
lung small cell carcinoma9.98e-074


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)

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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

No analysis results for this cluster

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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