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Coexpression cluster:C1023: Difference between revisions

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|tf_chipseq_enrich=NR3C1#2908;3:5.61488374918989:0.0129244394609099:0.0464620519364579!ZZZ3#26009;2:59.8533031088083:0.000479799893503641:0.00436724952742084
|tf_chipseq_enrich=NR3C1#2908;3:5.61488374918989:0.0129244394609099:0.0464620519364579!ZZZ3#26009;2:59.8533031088083:0.000479799893503641:0.00436724952742084
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,0.301904,1.20684,0.554663,0.19223,0.190005,0.154405,0.450635,1.45571,0.152895,0.543352,0.81316,0.863056,0.774423,0.698835,0.163559,0.0766963,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.469827,0.269459,0.339976,0.266487,0.481208,0.244807,0.174436,1.35754,0.413601,0.0547276,0.299183,0.0169887,0.371118,0.555735,0.440085,0.416595,0.822946,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.776738,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.0911419,1.03748,0.149081,0.138565,0.127753,0.730167,0.797419,0.989108,0.96869,0.745864,0.575394,0.19474,0.986227,0.0220225,0.0757344,1.81046,0.659621,1.59442,1.22073,0.959334,0.827657,1.87422,1.48306,0.672575,0.162291,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.0278613,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,4.61069,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,1.10364,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.593875,0.0510299,0.960402,0.53901,1.37178,1.36372,0.643609,0.786331,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,1.70957,1.40773,0.213234,2.33631,0.00340764
}}
}}

Revision as of 14:38, 26 November 2012


Full id: C1023_seminal_ductus_thyroid_pituitary_throat_small_epididymis



Phase1 CAGE Peaks

Hg19::chr12:97856575..97856589,+p@chr12:97856575..97856589
+
Hg19::chr12:97856596..97856615,+p@chr12:97856596..97856615
+
Hg19::chr12:97856637..97856647,+p@chr12:97856637..97856647
+
Hg19::chr12:97869376..97869380,+p@chr12:97869376..97869380
+
Hg19::chr12:97874189..97874200,+p@chr12:97874189..97874200
+
Hg19::chr12:97904646..97904653,+p@chr12:97904646..97904653
+
Hg19::chr12:97926446..97926450,+p@chr12:97926446..97926450
+
Hg19::chr12:97955435..97955440,+p@chr12:97955435..97955440
+


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>

Uber Anatomy
Ontology termp-valuen
neural tube1.62e-4456
neural rod1.62e-4456
future spinal cord1.62e-4456
neural keel1.62e-4456
adult organism1.46e-39114
regional part of nervous system4.63e-3953
regional part of brain4.63e-3953
neural plate5.47e-3982
presumptive neural plate5.47e-3982
neurectoderm1.34e-3686
central nervous system2.11e-3681
nervous system2.88e-3389
regional part of forebrain1.39e-3141
forebrain1.39e-3141
anterior neural tube1.39e-3141
future forebrain1.39e-3141
brain1.89e-3168
future brain1.89e-3168
ecto-epithelium8.98e-30104
pre-chordal neural plate1.65e-2861
brain grey matter2.46e-2534
gray matter2.46e-2534
telencephalon1.25e-2434
cerebral hemisphere4.05e-2432
structure with developmental contribution from neural crest1.39e-23132
regional part of telencephalon7.75e-2232
ectoderm-derived structure6.93e-21171
ectoderm6.93e-21171
presumptive ectoderm6.93e-21171
regional part of cerebral cortex3.00e-1922
cerebral cortex8.32e-1925
pallium8.32e-1925
neocortex8.68e-1920
brainstem4.40e-146
organ system subdivision5.31e-14223
posterior neural tube8.98e-1415
chordal neural plate8.98e-1415
parietal lobe1.08e-105
gland of diencephalon2.57e-104
neuroendocrine gland2.57e-104
anatomical cluster2.74e-10373
gyrus1.07e-086
segmental subdivision of hindbrain1.33e-0812
hindbrain1.33e-0812
presumptive hindbrain1.33e-0812
male genital duct1.40e-083
internal male genitalia1.40e-083
diencephalon1.59e-087
future diencephalon1.59e-087
tube1.78e-08192
ciliary epithelium2.65e-083
ciliary body2.65e-083
anatomical conduit4.54e-08240
neural nucleus5.78e-089
nucleus of brain5.78e-089
spinal cord6.38e-083
dorsal region element6.38e-083
dorsum6.38e-083
pons6.83e-083
medulla oblongata7.32e-083
myelencephalon7.32e-083
future myelencephalon7.32e-083
segmental subdivision of nervous system7.59e-0813
male reproductive organ4.47e-0711
multi-tissue structure6.44e-07342


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
NR3C1#290835.614883749189890.01292443946090990.0464620519364579
ZZZ3#26009259.85330310880830.0004797998935036410.00436724952742084



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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