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Coexpression cluster:C3159: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.211629,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;0.752137,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:10, 22 January 2013


Full id: C3159_cerebellum_parietal_hippocampus_temporal_insula_frontal_postcentral



Phase1 CAGE Peaks

Hg19::chr11:47616191..47616196,-p7@C1QTNF4
Hg19::chr17:40834385..40834392,+p6@CNTNAP1
Hg19::chr19:49941642..49941657,-p6@SLC17A7


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:0015319sodium:inorganic phosphate symporter activity0.00706464146944542
GO:0015321sodium-dependent phosphate transmembrane transporter activity0.0164812521182351
GO:0005436sodium:phosphate symporter activity0.0164812521182351
GO:0015114phosphate transmembrane transporter activity0.0247167840339703
GO:0016493C-C chemokine receptor activity0.0275212931074951
GO:0019957C-C chemokine binding0.0275212931074951
GO:0001637G-protein chemoattractant receptor activity0.0275212931074951
GO:0004950chemokine receptor activity0.0275212931074951
GO:0019956chemokine binding0.0275212931074951
GO:0015296anion:cation symporter activity0.0275212931074951
GO:0005070SH3/SH2 adaptor activity0.0314253212205132
GO:0060090molecular adaptor activity0.0333704452132086
GO:0051480cytosolic calcium ion homeostasis0.0333704452132086
GO:0007204elevation of cytosolic calcium ion concentration0.0333704452132086
GO:0015103inorganic anion transmembrane transporter activity0.0333704452132086
GO:0030674protein binding, bridging0.0385573711424084
GO:0019955cytokine binding0.0385573711424084
GO:0015294solute:cation symporter activity0.0385573711424084
GO:0055074calcium ion homeostasis0.0385573711424084
GO:0006874cellular calcium ion homeostasis0.0385573711424084
GO:0006875cellular metal ion homeostasis0.0385573711424084
GO:0055065metal ion homeostasis0.0385573711424084
GO:0006817phosphate transport0.0385573711424084
GO:0042330taxis0.0385573711424084
GO:0006935chemotaxis0.0385573711424084
GO:0001653peptide receptor activity0.0385573711424084
GO:0008528peptide receptor activity, G-protein coupled0.0385573711424084
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.042863844773248
GO:0007626locomotory behavior0.042863844773248
GO:0055066di-, tri-valent inorganic cation homeostasis0.042863844773248
GO:0030003cellular cation homeostasis0.0431614103442473
GO:0055080cation homeostasis0.0431614103442473
GO:0042277peptide binding0.0431614103442473
GO:0008509anion transmembrane transporter activity0.0431614103442473
GO:0055082cellular chemical homeostasis0.0458795432522604
GO:0006873cellular ion homeostasis0.0458795432522604
GO:0015293symporter activity0.0458795432522604
GO:0015698inorganic anion transport0.0479694248685004
GO:0050801ion homeostasis0.0479878942586728



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
regional part of nervous system1.74e-8353
regional part of brain1.74e-8353
neural tube7.95e-7956
neural rod7.95e-7956
future spinal cord7.95e-7956
neural keel7.95e-7956
brain2.80e-7368
future brain2.80e-7368
telencephalon2.41e-6634
regional part of forebrain3.77e-6641
forebrain3.77e-6641
anterior neural tube3.77e-6641
future forebrain3.77e-6641
regional part of cerebral cortex7.87e-6622
central nervous system2.64e-6581
cerebral hemisphere8.89e-6432
brain grey matter9.48e-6034
gray matter9.48e-6034
nervous system2.13e-5889
cerebral cortex7.41e-5825
pallium7.41e-5825
regional part of telencephalon4.73e-5732
neocortex3.63e-5520
neural plate1.58e-5282
presumptive neural plate1.58e-5282
neurectoderm7.08e-5086
adult organism4.55e-46114
pre-chordal neural plate2.23e-4361
ecto-epithelium1.96e-40104
structure with developmental contribution from neural crest2.35e-33132
ectoderm-derived structure2.50e-28171
ectoderm2.50e-28171
presumptive ectoderm2.50e-28171
gyrus7.53e-266
organ system subdivision4.34e-22223
parietal lobe1.28e-205
limbic system5.11e-205
tube1.40e-19192
segmental subdivision of hindbrain1.10e-1712
hindbrain1.10e-1712
presumptive hindbrain1.10e-1712
regional part of metencephalon7.53e-179
metencephalon7.53e-179
future metencephalon7.53e-179
segmental subdivision of nervous system2.76e-1613
anatomical conduit1.32e-14240
temporal lobe1.61e-146
posterior neural tube4.79e-1415
chordal neural plate4.79e-1415
middle temporal gyrus1.61e-132
Ammon's horn1.71e-132
lobe parts of cerebral cortex1.71e-132
hippocampal formation1.71e-132
limbic lobe1.71e-132
organ part1.33e-12218
occipital lobe1.86e-115
anatomical cluster5.04e-11373
epithelium2.72e-10306
cell layer3.87e-10309
cerebellum4.61e-106
rhombic lip4.61e-106
multi-tissue structure1.60e-09342
frontal cortex2.43e-093
brainstem2.77e-096
pons1.05e-083
postcentral gyrus1.18e-071
insula1.25e-071
nucleus accumbens1.33e-071
ventral striatum1.33e-071
paracentral gyrus1.51e-071
occipital pole1.83e-071
pole of cerebral hemisphere1.83e-071
olfactory region2.07e-071
primary subdivision of skull2.07e-071
cranium2.07e-071
neurocranium2.07e-071
chondrocranium2.07e-071
cartilaginous neurocranium2.07e-071
head paraxial mesoderm2.07e-071
corpus callosum4.34e-071
central nervous system cell part cluster4.34e-071
axon tract4.34e-071
intercerebral commissure4.34e-071
dorsal telencephalic commissure4.34e-071
brain white matter4.34e-071
brain commissure4.34e-071
white matter4.34e-071
nervous system commissure4.34e-071
cerebral hemisphere white matter4.34e-071
corpus striatum5.38e-074
striatum5.38e-074
ventral part of telencephalon5.38e-074
future corpus striatum5.38e-074


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
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
MA0144.11.31729
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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

No analysis results for this cluster

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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3159&oldid=2571670"