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Coexpression cluster:C334: Difference between revisions

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|tf_chipseq_enrich=NFE2#4778;4:9.0828541943093:0.000955074056277887:0.00687530875128248!NFYB#4801;7:3.45054566984574:0.00346435537471603:0.0176005161735646!NR2C2#7182;5:4.79626630959425:0.003585427593585:0.0181608454554743!POLR2A#5430;25:1.57900968864564:0.00131139902386779:0.0087846323297882!TBP#6908;17:1.85338534354819:0.00353755986200671:0.0179497262026002!YY1#7528;13:1.87780058082647:0.0126118953453923:0.0456021928395452!ZEB1#6935;7:3.47703012125903:0.00332015686360625:0.017172833928198
|tf_chipseq_enrich=NFE2#4778;4:9.0828541943093:0.000955074056277887:0.00687530875128248!NFYB#4801;7:3.45054566984574:0.00346435537471603:0.0176005161735646!NR2C2#7182;5:4.79626630959425:0.003585427593585:0.0181608454554743!POLR2A#5430;25:1.57900968864564:0.00131139902386779:0.0087846323297882!TBP#6908;17:1.85338534354819:0.00353755986200671:0.0179497262026002!YY1#7528;13:1.87780058082647:0.0126118953453923:0.0456021928395452!ZEB1#6935;7:3.47703012125903:0.00332015686360625:0.017172833928198
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459711,0.0531663,0.938433,0.163659,0.750463,0.703995,0.0961296,0.0863059,0.180591,0.632418,0.333813,0.54891,0.30591,0.168769,0.0741539,0.0520239,0.680905,0.083688,0.626203,0.167972,0.859206,0.0721663,0.566566,0.152606,0.122025,0.319868,0.179284,0.306894,0.29777,0.00694694,0.266967,0.250104
|tfbs_overrepresentation_for_novel_motifs=1.82659,2.17492,0.584729,0.0875053,0.101662,0.292862,0.785405,0.09085,0.346227,2.28811,1.38905,0.148731,1.77208,0.377328,0.10059,0.286634,0.73324,0.0132576,0.140042,0.430589,0.0341522,0.206646,0.593527,0.241549,0.407145,0.487936,0.182286,0.588774,1.53567,0.601202,0.498615,0.292383,2.15328,0.392661,0.196304,1.78558,1.69487,0.613203,0.0594165,0.479051,0.075382,0.212479,0.519803,0.0994069,0.137997,0.166385,0.394651,1.34244,0.220986,0.255039,0.981244,0.8161,0.258779,0.925826,0.475837,0.381341,0.262028,0.337373,0.411545,0.686673,0.864021,0.397937,0.0297555,0.245859,0.423138,0.222166,0.551996,0.889382,0.284717,0.737624,1.64407,0.096729,6.88574,0.474142,1.06624,0.715827,0.281192,0.234122,0.282332,0.395197,0.147738,0.245107,0.136039,0.093723,1.10124,4.17358,1.54817,0.573862,0.548595,0.984017,0.634935,1.05302,0.304922,0.275832,5.58301,0.151139,0.258701,0.337414,0.1899,1.17796,0.160851,0.300686,0.333104,0.268157,0.214431,0.912291,0.713226,0.116603,1.5586,1.41805,0.341703,0.881325,0.569154,0.565106,0.592003,0.189368,1.25255,0.853712,0.628771,0.28206,0.467142,0.185428,0.289431,0.14239,1.65287,0.661753,0.770379,0.30868,0.503421,0.307146,0.409436,0.504593,0.515797,0.140501,0.646547,0.362999,0.223949,0.281279,0.608436,1.42699,1.03434,0.575287,0.122045,0.334687,0.215605,0.099088,0.204563,1.27059,0.0572348,0.463809,0.0646042,6.69618,0.409747,0.517992,1.28989,0.765951,0.176807,0.0909941,0.0482085,0.352379,0.574213,0.394694,0.281754,0.642794,0.226459,0.135598,0.243222,0.391301,0.847914
}}
}}

Revision as of 14:08, 26 November 2012


Full id: C334_cerebellum_pineal_occipital_pituitary_amygdala_medial_caudate



Phase1 CAGE Peaks

Hg19::chr10:101190668..101190736,+p1@ENST00000416191
Hg19::chr11:17230061..17230092,+p@chr11:17230061..17230092
+
Hg19::chr11:57417405..57417423,-p2@YPEL4
Hg19::chr12:118406777..118406811,-p1@KSR2
Hg19::chr12:79258463..79258477,+p10@SYT1
Hg19::chr12:9066766..9066866,+p1@PHC1
Hg19::chr13:25542609..25542639,-p1@TPTE2P1
Hg19::chr13:29394076..29394108,+p@chr13:29394076..29394108
+
Hg19::chr14:100070869..100070889,+p1@ENST00000502101
Hg19::chr14:103524166..103524207,+p1@AK057714
Hg19::chr14:58797974..58798011,+p3@ARID4A
Hg19::chr14:66975213..66975239,+p2@GPHN
Hg19::chr14:94024982..94024986,+p@chr14:94024982..94024986
+
Hg19::chr15:61521462..61521482,-p4@RORA
Hg19::chr15:65204075..65204119,+p1@ANKDD1A
Hg19::chr17:50235645..50235676,-p2@CA10
Hg19::chr18:29265423..29265443,-p@chr18:29265423..29265443
-
Hg19::chr19:28284917..28284960,+p1@AK095009
Hg19::chr19:44406012..44406044,+p@chr19:44406012..44406044
+
Hg19::chr1:147719007..147719042,-p@chr1:147719007..147719042
-
Hg19::chr1:197237324..197237332,+p5@CRB1
Hg19::chr20:5892037..5892067,+p2@CHGB
Hg19::chr21:17442799..17442832,+p17@LINC00478
Hg19::chr21:17443471..17443515,+p10@LINC00478
Hg19::chr22:20850171..20850221,+p3@MED15
Hg19::chr4:176987131..176987162,+p2@WDR17
Hg19::chr4:176987163..176987196,+p3@WDR17
Hg19::chr4:57276661..57276679,+p1@ENST00000416157
Hg19::chr5:139487724..139487763,+p@chr5:139487724..139487763
+
Hg19::chr5:161494464..161494499,+p4@GABRG2
Hg19::chr6:46620738..46620755,+p2@SLC25A27
Hg19::chr6:80247381..80247389,+p@chr6:80247381..80247389
+
Hg19::chrX:46988715..46988759,+p@chrX:46988715..46988759
+
Hg19::chrX:83443478..83443513,-p@chrX:83443478..83443513
-


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

p.valueFDRnGenesnPathwayName
6.75939345257143e-050.0427869605547771222{DNM1,22} (Static Module):NA



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
neural cell9.88e-0925
neuronal stem cell1.26e-078
Uber Anatomy
Ontology termp-valuen
nervous system1.14e-6589
central nervous system5.13e-6281
adult organism4.59e-61114
neural tube6.06e-6056
neural rod6.06e-6056
future spinal cord6.06e-6056
neural keel6.06e-6056
regional part of nervous system1.22e-5653
regional part of brain1.22e-5653
brain6.10e-5068
future brain6.10e-5068
regional part of forebrain2.47e-4841
forebrain2.47e-4841
anterior neural tube2.47e-4841
future forebrain2.47e-4841
neural plate2.62e-4882
presumptive neural plate2.62e-4882
neurectoderm1.01e-4786
brain grey matter8.22e-4034
gray matter8.22e-4034
telencephalon8.96e-4034
ectoderm-derived structure1.29e-39171
ectoderm1.29e-39171
presumptive ectoderm1.29e-39171
pre-chordal neural plate3.41e-3861
cerebral hemisphere9.91e-3832
regional part of telencephalon1.36e-3732
organ system subdivision3.70e-37223
ecto-epithelium4.06e-37104
structure with developmental contribution from neural crest5.81e-34132
cerebral cortex1.74e-2925
pallium1.74e-2925
regional part of cerebral cortex1.02e-2722
neocortex2.28e-2520
anatomical cluster1.12e-23373
organ part9.67e-15218
multi-tissue structure4.03e-14342
embryo4.74e-14592
tube1.13e-12192
posterior neural tube1.37e-1215
chordal neural plate1.37e-1215
developing anatomical structure4.88e-12581
basal ganglion7.48e-129
nuclear complex of neuraxis7.48e-129
aggregate regional part of brain7.48e-129
collection of basal ganglia7.48e-129
cerebral subcortex7.48e-129
embryonic structure9.47e-12564
multi-cellular organism1.06e-11656
anatomical conduit1.12e-11240
neural nucleus1.24e-119
nucleus of brain1.24e-119
germ layer1.26e-11560
germ layer / neural crest1.26e-11560
embryonic tissue1.26e-11560
presumptive structure1.26e-11560
germ layer / neural crest derived structure1.26e-11560
epiblast (generic)1.26e-11560
segmental subdivision of nervous system1.38e-1013
diencephalon8.35e-107
future diencephalon8.35e-107
organ1.21e-09503
segmental subdivision of hindbrain1.24e-0912
hindbrain1.24e-0912
presumptive hindbrain1.24e-0912
epithelium1.44e-09306
telencephalic nucleus1.66e-097
anatomical system1.86e-09624
anatomical group2.26e-09625
cell layer3.07e-09309
temporal lobe4.14e-096
gyrus1.23e-086
brainstem6.10e-086
limbic system2.08e-075
parietal lobe2.13e-075
occipital lobe2.30e-075


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
NFE2#477849.08285419430930.0009550740562778870.00687530875128248
NFYB#480173.450545669845740.003464355374716030.0176005161735646
NR2C2#718254.796266309594250.0035854275935850.0181608454554743
POLR2A#5430251.579009688645640.001311399023867790.0087846323297882
TBP#6908171.853385343548190.003537559862006710.0179497262026002
YY1#7528131.877800580826470.01261189534539230.0456021928395452
ZEB1#693573.477030121259030.003320156863606250.017172833928198



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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