Coexpression cluster:C3575: Difference between revisions

Revision as of 16:12, 26 November 2012

Full id: C3575_liver_Hepatocyte_testicular_Placental_colon_hepatoblastoma_acute

Phase1 CAGE Peaks

Hg19::chr16:56691838..56691862,+	p3@MT1F
Hg19::chr16:56691864..56691879,+	p2@MT1F
Hg19::chr16:56691911..56691929,+	p4@MT1F

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset uberon_data

Uber Anatomy
Ontology term	p-value	n
neural tube	4.53e-21	56
neural rod	4.53e-21	56
future spinal cord	4.53e-21	56
neural keel	4.53e-21	56
central nervous system	8.26e-21	81
adult organism	1.34e-20	114
regional part of nervous system	2.05e-19	53
regional part of brain	2.05e-19	53
nervous system	5.43e-17	89
brain	1.40e-16	68
future brain	1.40e-16	68
regional part of forebrain	8.15e-15	41
forebrain	8.15e-15	41
anterior neural tube	8.15e-15	41
future forebrain	8.15e-15	41
brain grey matter	2.86e-13	34
gray matter	2.86e-13	34
telencephalon	4.55e-13	34
neurectoderm	8.77e-13	86
neural plate	9.48e-13	82
presumptive neural plate	9.48e-13	82
organ system subdivision	2.26e-12	223
regional part of telencephalon	2.76e-12	32
cerebral hemisphere	3.06e-12	32
ecto-epithelium	4.66e-11	104
regional part of cerebral cortex	5.60e-10	22
pre-chordal neural plate	1.56e-09	61
cerebral cortex	2.27e-09	25
pallium	2.27e-09	25
neocortex	5.16e-09	20
posterior neural tube	1.45e-07	15
chordal neural plate	1.45e-07	15
ectoderm-derived structure	2.04e-07	171
ectoderm	2.04e-07	171
presumptive ectoderm	2.04e-07	171

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461474109480173
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580681848192912
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179709855164067
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00308524034557343
REST#5978	3	9.65002871612802	0.00111263624711459	0.00766609163559841
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308682846147405
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.006423069190692
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242462839103775

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 8: / Line 8: @@
 |tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461474109480173!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580681848192912!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179709855164067!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308524034557343!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766609163559841!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308682846147405!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.006423069190692!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242462839103775
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+|tfbs_overrepresentation_for_novel_motifs=0.699513,2.0185,4.0284,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,3.05144,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.92922,1.06461,1.02656,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,3.76231,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,1.63757,0.830777,1.58942,2.46882,3.13442,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,2.15653,1.96295
 }}

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Coexpression cluster:C3575: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:12, 26 November 2012

Phase1 CAGE Peaks

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