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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:23, 17 September 2013


Full id: C445_lung_Lens_Ciliary_diencephalon_thalamus_bile_hepatoma



Phase1 CAGE Peaks

Hg19::chr11:31014065..31014073,-p1@DCDC5
Hg19::chr15:52161504..52161511,+p@chr15:52161504..52161511
+
Hg19::chr15:99387143..99387153,-p@chr15:99387143..99387153
-
Hg19::chr1:114654778..114654823,+p@chr1:114654778..114654823
+
Hg19::chr20:388056..388067,+p10@RBCK1
Hg19::chr3:178968900..178968909,-p5@KCNMB3
Hg19::chr5:175298120..175298129,-p@chr5:175298120..175298129
-
Hg19::chr5:175298177..175298187,+p38@CPLX2
Hg19::chr7:107883547..107883552,-p30@NRCAM
Hg19::chr7:107883582..107883593,-p20@NRCAM
Hg19::chr7:107883608..107883632,-p15@NRCAM
Hg19::chr7:107883640..107883652,-p21@NRCAM
Hg19::chr7:107883678..107883689,-p13@NRCAM
Hg19::chr7:107883711..107883718,-p29@NRCAM
Hg19::chr7:107883761..107883772,-p18@NRCAM
Hg19::chr7:107883776..107883779,-p37@NRCAM
Hg19::chr7:107883785..107883799,-p12@NRCAM
Hg19::chr7:107883809..107883820,-p11@NRCAM
Hg19::chr7:107883821..107883841,-p7@NRCAM
Hg19::chr7:11676048..11676067,-p23@THSD7A
Hg19::chr7:134212246..134212265,+p3@AKR1B10
Hg19::chr7:134220360..134220368,+p@chr7:134220360..134220368
+


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:0045162clustering of voltage-gated sodium channels0.0269574158313691
GO:0045666positive regulation of neuron differentiation0.0269574158313691
GO:0019228generation of action potential0.0269574158313691
GO:0045161neuronal ion channel clustering0.0269574158313691
GO:0007413axonal fasciculation0.0269574158313691
GO:0030506ankyrin binding0.0269574158313691
GO:0043303mast cell degranulation0.0269574158313691
GO:0002448mast cell mediated immunity0.0269574158313691
GO:0045576mast cell activation0.0269574158313691
GO:0043299leukocyte degranulation0.0269574158313691
GO:0005513detection of calcium ion0.0269574158313691
GO:0002444myeloid leukocyte mediated immunity0.027790017114087
GO:0042551neuron maturation0.027790017114087
GO:0008038neuron recognition0.027790017114087
GO:0030516regulation of axon extension0.027790017114087
GO:0004033aldo-keto reductase activity0.027790017114087
GO:0048675axon extension0.0350845861841104
GO:0015459potassium channel regulator activity0.0350845861841104
GO:0009593detection of chemical stimulus0.0350845861841104
GO:0019905syntaxin binding0.0351789369391645
GO:0000149SNARE binding0.0370239210486011
GO:0006081aldehyde metabolic process0.0379096057419114
GO:0007416synaptogenesis0.0379096057419114
GO:0050770regulation of axonogenesis0.0379096057419114
GO:0045664regulation of neuron differentiation0.0379096057419114
GO:0002274myeloid leukocyte activation0.0379096057419114
GO:0042391regulation of membrane potential0.0379096057419114
GO:0015269calcium-activated potassium channel activity0.0379096057419114
GO:0022839ion gated channel activity0.0379096057419114
GO:0006904vesicle docking during exocytosis0.0379096057419114
GO:0005227calcium activated cation channel activity0.0379096057419114
GO:0016247channel regulator activity0.0379096057419114
GO:0001764neuron migration0.0379096057419114
GO:0048278vesicle docking0.0379096057419114
GO:0008037cell recognition0.0379096057419114
GO:0022406membrane docking0.0379096057419114
GO:0050767regulation of neurogenesis0.0379096057419114
GO:0050808synapse organization and biogenesis0.0379096057419114
GO:0001508regulation of action potential0.0379096057419114
GO:0048469cell maturation0.0415637487495041
GO:0045597positive regulation of cell differentiation0.0423447442564664
GO:0009897external side of plasma membrane0.0439633943978233
GO:0045055regulated secretory pathway0.0444711836814443
GO:0021700developmental maturation0.0444711836814443



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
pigment epithelium of eye2.17e-1511
ciliary epithelium1.40e-143
ciliary body1.40e-143
medulla oblongata1.83e-143
myelencephalon1.83e-143
future myelencephalon1.83e-143
anterior segment of eyeball2.51e-1214
atypical epithelium2.80e-114
cuboidal epithelium3.79e-114
transparent eye structure3.79e-114
simple cuboidal epithelium3.79e-114
cranial placode3.79e-114
lens of camera-type eye3.79e-114
epithelium of lens3.79e-114
lens placode3.79e-114
lens vesicle3.79e-114
camera-type eye6.17e-0920
simple eye6.17e-0920
immature eye6.17e-0920
ocular region6.17e-0920
eyeball of camera-type eye6.17e-0920
optic cup6.17e-0920
optic vesicle6.17e-0920
eye primordium6.17e-0920
eye1.48e-0821
visual system1.48e-0821
neural plate2.75e-0882
presumptive neural plate2.75e-0882
face3.27e-0822
vasculature of eye5.92e-086
uvea5.92e-086
vasculature of head5.92e-086
neurectoderm6.20e-0886
brainstem6.78e-086
sense organ1.31e-0724
sensory system1.31e-0724
entire sense organ system1.31e-0724
organ segment4.02e-0798
diencephalon5.70e-077
future diencephalon5.70e-077


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)
MA0003.13.88725e-06
MA0004.10.158412
MA0006.10.0694838
MA0007.10.449227
MA0009.10.526253
MA0014.10.000136754
MA0017.11.53695
MA0019.11.33677
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.11.21054
MA0040.10.456051
MA0041.10.508527
MA0042.10.457543
MA0043.10.526535
MA0046.10.516541
MA0048.10.0283321
MA0050.10.458935
MA0051.10.22589
MA0052.10.459414
MA0055.10.00831201
MA0056.10
MA0057.10.0785329
MA0058.10.101748
MA0059.10.101051
MA0060.10.0258987
MA0061.10.412126
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.149869
MA0069.10.51311
MA0070.15.54064
MA0071.10.201311
MA0072.10.499187
MA0073.18.19445e-08
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.101139
MA0083.10.532971
MA0084.10.999884
MA0087.12.15111
MA0088.10.154793
MA0089.10
MA0090.11.24237
MA0091.10.160096
MA0092.10.4236
MA0093.10.0708814
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.25283
MA0103.10.232452
MA0105.10.274046
MA0106.10.259598
MA0107.10.041912
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.272101
MA0114.11.00251
MA0115.11.76919
MA0116.10.0431675
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.234116
MA0139.10.0745458
MA0140.10.199454
MA0141.10.100114
MA0142.10.359701
MA0143.10.272236
MA0144.10.0352516
MA0145.10.0380521
MA0146.10.000466837
MA0147.10.0444528
MA0148.10.99741
MA0149.10.192747
MA0062.20.0177333
MA0035.20.198962
MA0039.27.69028e-06
MA0138.20.302079
MA0002.20.0984982
MA0137.20.0801516
MA0104.20.0256869
MA0047.20.698519
MA0112.20.00138028
MA0065.20.0116842
MA0150.10.369323
MA0151.10
MA0152.14.1306
MA0153.10.615584
MA0154.10.00323928
MA0155.10.0746593
MA0156.10.277694
MA0157.10.337287
MA0158.10
MA0159.10.170777
MA0160.10.18494
MA0161.10
MA0162.15.0328e-05
MA0163.10.0253576
MA0164.11.40716
MA0080.20.0709213
MA0018.25.70538
MA0099.23.27111
MA0079.21.38049e-07
MA0102.21.03595
MA0258.10.032189
MA0259.10.0476147
MA0442.10



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
FOXA2#317044.478266136848230.01104661864274050.0406346084963785



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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