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Coexpression cluster:C1127: Difference between revisions

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|tf_chipseq_enrich=FOXA1#3169;4:6.33223985679169:0.00185468101692017:0.0109423246371102!HEY1#23462;5:2.88579360221836:0.0123136694185303:0.0446196419541282!NANOG#79923;3:12.5334764918626:0.00126105218950347:0.00846801450649734!NRF1#4899;4:6.97730254154909:0.0012853142886222:0.00861874407636685
|tf_chipseq_enrich=FOXA1#3169;4:6.33223985679169:0.00185468101692017:0.0109423246371102!HEY1#23462;5:2.88579360221836:0.0123136694185303:0.0446196419541282!NANOG#79923;3:12.5334764918626:0.00126105218950347:0.00846801450649734!NRF1#4899;4:6.97730254154909:0.0012853142886222:0.00861874407636685
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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.465735,0.384703,0.529489,1.62733,0.52784,0.604235,0.226729,0.224331,0.443077,0.497563,0.647852,1.03506,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.32524,0.384762,0.23059,0.520063,0.897212,0.430372,2.71467,0.164928,0.517892,0.346214,0.150685,0.475674,0.864517,0.714156,0.546594,0.309012,0.021349,2.27897,0.529001,0.282922,1.12779,0.307642,0.459366,0.541549,0.340293,0.0257952,1.06715,0.60533,0.486696,0.876276,0.346342,0.684981,1.49721,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,1.2198,1.0929,0.179863,0.971313,0.156354,0.782748,0.850825,1.90717,1.099,0.798651,2.56965,0.229431,1.04131,0.567403,1.62218,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,2.13136,0.715799,0.413337,0.28424,0.875714,0.918549,0.831244,1.78098,0.493026,0.815341,0.589207,0.43012,1.57162,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.642446,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,2.59532,1.28996,1.37933,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.722945,0.106334,0.518684,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.695791,0.602897,0.0992692
}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1127_cerebellum_substantia_spinal_thalamus_medulla_occipital_globus



Phase1 CAGE Peaks

Hg19::chr11:105948129..105948161,-p2@KBTBD3
Hg19::chr17:36729056..36729072,-p8@SRCIN1
Hg19::chr17:66201593..66201646,+p@chr17:66201593..66201646
+
Hg19::chr1:171911363..171911369,+p@chr1:171911363..171911369
+
Hg19::chr3:129407466..129407477,-p19@TMCC1
Hg19::chr3:129407485..129407505,-p5@TMCC1
Hg19::chr3:129407535..129407543,-p21@TMCC1


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
embryonic stem cell3.34e-085
Uber Anatomy
Ontology termp-valuen
neural tube1.17e-7756
neural rod1.17e-7756
future spinal cord1.17e-7756
neural keel1.17e-7756
regional part of nervous system4.60e-7253
regional part of brain4.60e-7253
adult organism2.22e-67114
central nervous system1.37e-6681
nervous system5.19e-6589
regional part of forebrain1.42e-5941
forebrain1.42e-5941
anterior neural tube1.42e-5941
future forebrain1.42e-5941
neural plate2.19e-5982
presumptive neural plate2.19e-5982
brain3.71e-5768
future brain3.71e-5768
neurectoderm7.94e-5686
brain grey matter2.15e-4734
gray matter2.15e-4734
telencephalon3.10e-4734
ecto-epithelium6.18e-45104
regional part of telencephalon1.43e-4332
cerebral hemisphere1.98e-4332
pre-chordal neural plate8.51e-4361
structure with developmental contribution from neural crest3.28e-37132
organ system subdivision2.24e-34223
regional part of cerebral cortex2.15e-3322
cerebral cortex1.92e-3125
pallium1.92e-3125
ectoderm-derived structure2.86e-31171
ectoderm2.86e-31171
presumptive ectoderm2.86e-31171
neocortex5.44e-3020
tube8.95e-25192
posterior neural tube2.28e-1815
chordal neural plate2.28e-1815
anatomical conduit9.02e-18240
anatomical cluster9.15e-18373
neural nucleus1.30e-179
nucleus of brain1.30e-179
basal ganglion3.84e-179
nuclear complex of neuraxis3.84e-179
aggregate regional part of brain3.84e-179
collection of basal ganglia3.84e-179
cerebral subcortex3.84e-179
segmental subdivision of nervous system5.67e-1513
epithelium2.84e-14306
cell layer6.01e-14309
telencephalic nucleus8.30e-147
diencephalon1.31e-137
future diencephalon1.31e-137
segmental subdivision of hindbrain2.42e-1312
hindbrain2.42e-1312
presumptive hindbrain2.42e-1312
brainstem9.33e-136
multi-tissue structure3.27e-12342
gyrus4.12e-126
organ part1.56e-10218
parietal lobe3.30e-105
limbic system4.55e-105
occipital lobe5.58e-105
embryo2.53e-09592
regional part of metencephalon2.15e-089
metencephalon2.15e-089
future metencephalon2.15e-089
corpus striatum2.82e-084
striatum2.82e-084
ventral part of telencephalon2.82e-084
future corpus striatum2.82e-084
regional part of diencephalon3.04e-084
organ3.22e-08503
gland of diencephalon4.09e-084
neuroendocrine gland4.09e-084
germ layer9.88e-08560
germ layer / neural crest9.88e-08560
embryonic tissue9.88e-08560
presumptive structure9.88e-08560
germ layer / neural crest derived structure9.88e-08560
epiblast (generic)9.88e-08560
embryonic structure1.63e-07564
multi-cellular organism2.18e-07656
pons2.64e-073
medulla oblongata4.17e-073
myelencephalon4.17e-073
future myelencephalon4.17e-073
developing anatomical structure4.87e-07581
spinal cord6.04e-073
dorsal region element6.04e-073
dorsum6.04e-073
temporal lobe6.37e-076
frontal cortex6.79e-073


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
FOXA1#316946.332239856791690.001854681016920170.0109423246371102
HEY1#2346252.885793602218360.01231366941853030.0446196419541282
NANOG#79923312.53347649186260.001261052189503470.00846801450649734
NRF1#489946.977302541549090.00128531428862220.00861874407636685



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.