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Coexpression cluster:C4131: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0229993218275533!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183905529888971!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268450140053649!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.032490583795699!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329232838293688
|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0229993218275533!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183905529888971!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268450140053649!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.032490583795699!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329232838293688
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,2.63304,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,2.26789,0.993996,2.39382,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,1.73097,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135
}}
}}

Revision as of 16:34, 26 November 2012


Full id: C4131_Mast_corpus_optic_thalamus_substantia_spinal_globus



Phase1 CAGE Peaks

Hg19::chr2:145188503..145188517,-p40@ZEB2
Hg19::chr2:145188568..145188590,-p27@ZEB2
Hg19::chr4:48782217..48782228,-p2@FRYL


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:0046332SMAD binding0.0480289559837234



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube1.36e-5056
neural rod1.36e-5056
future spinal cord1.36e-5056
neural keel1.36e-5056
regional part of nervous system5.38e-4653
regional part of brain5.38e-4653
adult organism1.68e-44114
central nervous system1.77e-4281
nervous system2.55e-4089
telencephalon2.79e-3934
brain grey matter3.95e-3934
gray matter3.95e-3934
regional part of forebrain4.35e-3941
forebrain4.35e-3941
anterior neural tube4.35e-3941
future forebrain4.35e-3941
brain3.38e-3868
future brain3.38e-3868
neural plate4.28e-3782
presumptive neural plate4.28e-3782
regional part of telencephalon6.42e-3632
cerebral hemisphere8.79e-3632
neurectoderm1.15e-3486
pre-chordal neural plate2.76e-2661
ecto-epithelium4.43e-26104
regional part of cerebral cortex6.36e-2622
cerebral cortex1.21e-2425
pallium1.21e-2425
neocortex1.32e-2220
structure with developmental contribution from neural crest1.27e-21132
ectoderm-derived structure5.03e-17171
ectoderm5.03e-17171
presumptive ectoderm5.03e-17171
neural nucleus1.38e-169
nucleus of brain1.38e-169
basal ganglion1.81e-169
nuclear complex of neuraxis1.81e-169
aggregate regional part of brain1.81e-169
collection of basal ganglia1.81e-169
cerebral subcortex1.81e-169
organ system subdivision6.25e-16223
telencephalic nucleus2.31e-137
posterior neural tube2.50e-1215
chordal neural plate2.50e-1215
brainstem5.35e-116
limbic system6.77e-105
parietal lobe7.14e-105
segmental subdivision of nervous system9.93e-1013
tube5.37e-09192
segmental subdivision of hindbrain2.99e-0812
hindbrain2.99e-0812
presumptive hindbrain2.99e-0812
gyrus3.76e-086
corpus striatum4.64e-084
striatum4.64e-084
ventral part of telencephalon4.64e-084
future corpus striatum4.64e-084
organ2.36e-07503


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
BATF#10538216.23853452820240.004917462407809970.0229993218275533
BCL11A#53335218.91297006907140.003639406248379680.0183905529888971
IRF4#3662214.60967512449610.006056122473217890.0268450140053649
MEF2A#4205212.4954872730960.008235029478029740.032490583795699
TRIM28#10155212.39368336350830.008368344129438470.0329232838293688



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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