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Coexpression cluster:C3396

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Full id: C3396_brain_occipital_duodenum_temporal_parietal_small_Neurons



Phase1 CAGE Peaks

Hg19::chr14:103988483..103988543,-p3@CKB
Hg19::chr3:127347988..127348000,+p2@PODXL2
Hg19::chr3:127348005..127348063,+p1@PODXL2


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:0055064chloride ion homeostasis0.000883080183680678
GO:0055083monovalent inorganic anion homeostasis0.000883080183680678
GO:0030644cellular chloride ion homeostasis0.000883080183680678
GO:0030320cellular monovalent inorganic anion homeostasis0.000883080183680678
GO:0004111creatine kinase activity0.00282573181120752
GO:0055081anion homeostasis0.00302748067160046
GO:0030002cellular anion homeostasis0.00302748067160046
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0141228361494071
GO:0005539glycosaminoglycan binding0.0407066168659049
GO:0030247polysaccharide binding0.0407066168659049
GO:0001871pattern binding0.0407066168659049
GO:0007420brain development0.0408329421154592



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
nervous system2.81e-3389
central nervous system1.57e-3281
neural tube5.08e-2956
neural rod5.08e-2956
future spinal cord5.08e-2956
neural keel5.08e-2956
regional part of nervous system1.38e-2753
regional part of brain1.38e-2753
neurectoderm1.28e-2686
organ system subdivision1.46e-26223
brain3.91e-2668
future brain3.91e-2668
neural plate3.26e-2582
presumptive neural plate3.26e-2582
regional part of forebrain1.13e-2241
forebrain1.13e-2241
anterior neural tube1.13e-2241
future forebrain1.13e-2241
pre-chordal neural plate1.72e-2061
ecto-epithelium2.25e-20104
ectoderm-derived structure1.27e-19171
ectoderm1.27e-19171
presumptive ectoderm1.27e-19171
brain grey matter1.82e-1934
gray matter1.82e-1934
telencephalon3.15e-1934
cerebral hemisphere1.03e-1832
regional part of telencephalon1.74e-1832
adult organism9.20e-16114
anatomical cluster1.50e-15373
cerebral cortex2.98e-1525
pallium2.98e-1525
regional part of cerebral cortex3.03e-1422
neocortex4.38e-1320
organ part3.07e-12218
structure with developmental contribution from neural crest3.65e-11132
multi-tissue structure5.79e-10342
tube1.79e-08192
epithelium1.39e-07306
posterior neural tube1.53e-0715
chordal neural plate1.53e-0715
cell layer1.81e-07309
organ segment2.11e-0798
segmental subdivision of nervous system8.81e-0713
Disease
Ontology termp-valuen
cell type cancer1.31e-16143
carcinoma3.34e-15106
cancer1.20e-11235
disease of cellular proliferation2.00e-11239


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)
MA0003.14.57391
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.15.56064
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.14.37851
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.11.70014
MA0060.13.15662
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.11.70974
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.14.34338
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.24.10519
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
E2F1#186934.907389214879320.008460985347239390.0324277742634985
E2F6#187635.017155731697390.00791769806886330.0321182501597923
NFYA#4800212.28372046655370.008516011403724430.0324635440009335
NFYB#4801211.17319550235760.01025467135054530.0381134384761423
SETDB1#9869226.8800174520070.001814468907964410.0108915063094945
SP2#6668217.43568699589640.004273568481769740.0203097569470126



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.