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{{Coexpression_clusters
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|full_id=C652_cerebellum_occipital_pineal_pituitary_medial_parietal_amygdala
|id=C652
}}

Latest revision as of 11:27, 17 September 2013


Full id: C652_cerebellum_occipital_pineal_pituitary_medial_parietal_amygdala



Phase1 CAGE Peaks

Hg19::chr11:105948040..105948082,-p1@KBTBD3
Hg19::chr11:8190534..8190595,-p1@RIC3
Hg19::chr17:40897043..40897087,-p1@EZH1
Hg19::chr17:5095296..5095308,+p2@LOC100130950
Hg19::chr19:38085739..38085762,+p3@ZNF540
Hg19::chr19:38085768..38085821,+p1@ZNF540
Hg19::chr1:244998602..244998646,+p3@FAM36A
Hg19::chr3:108308331..108308389,+p2@DZIP3
Hg19::chr4:149363637..149363651,-p4@NR3C2
Hg19::chr4:149363662..149363688,-p6@NR3C2
Hg19::chr6:117002339..117002400,+p1@KPNA5
Hg19::chr6:27342978..27343050,-p1@ZNF204P
Hg19::chr8:119634141..119634223,-p1@SAMD12


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:0031593polyubiquitin binding0.0282241442524776
GO:0055078sodium ion homeostasis0.0282241442524776
GO:0006883cellular sodium ion homeostasis0.0282241442524776
GO:0012505endomembrane system0.0302301958653872
GO:0000209protein polyubiquitination0.0398664843190308
GO:0006607NLS-bearing substrate import into nucleus0.0398664843190308
GO:0031090organelle membrane0.0398664843190308
GO:0030004cellular monovalent inorganic cation homeostasis0.0398664843190308
GO:0055067monovalent inorganic cation homeostasis0.0398664843190308
GO:0043130ubiquitin binding0.0398664843190308
GO:0032182small conjugating protein binding0.0398664843190308
GO:0005789endoplasmic reticulum membrane0.0398664843190308
GO:0042175nuclear envelope-endoplasmic reticulum network0.0398664843190308
GO:0044432endoplasmic reticulum part0.0456690194223664



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>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell6.87e-1052
lymphocyte1.12e-0953
common lymphoid progenitor1.12e-0953
nucleate cell2.82e-0955
mature alpha-beta T cell7.28e-0918
alpha-beta T cell7.28e-0918
immature T cell7.28e-0918
mature T cell7.28e-0918
immature alpha-beta T cell7.28e-0918
T cell8.99e-0725
pro-T cell8.99e-0725
Uber Anatomy
Ontology termp-valuen
adult organism5.04e-53114
neural tube1.15e-3056
neural rod1.15e-3056
future spinal cord1.15e-3056
neural keel1.15e-3056
regional part of nervous system6.05e-2953
regional part of brain6.05e-2953
central nervous system7.06e-2881
nervous system3.69e-2789
regional part of forebrain8.43e-2641
forebrain8.43e-2641
anterior neural tube8.43e-2641
future forebrain8.43e-2641
brain3.57e-2568
future brain3.57e-2568
neurectoderm1.50e-2186
brain grey matter4.09e-2134
gray matter4.09e-2134
telencephalon4.26e-2134
neural plate6.40e-2182
presumptive neural plate6.40e-2182
cerebral hemisphere5.94e-2032
regional part of telencephalon6.18e-2032
pre-chordal neural plate1.57e-1661
regional part of cerebral cortex8.15e-1622
cerebral cortex1.72e-1525
pallium1.72e-1525
organ system subdivision2.53e-15223
neocortex1.50e-1420
ecto-epithelium4.31e-14104
ectoderm-derived structure4.42e-14171
ectoderm4.42e-14171
presumptive ectoderm4.42e-14171
structure with developmental contribution from neural crest1.27e-09132
basal ganglion3.28e-079
nuclear complex of neuraxis3.28e-079
aggregate regional part of brain3.28e-079
collection of basal ganglia3.28e-079
cerebral subcortex3.28e-079
neural nucleus4.24e-079
nucleus of brain4.24e-079


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)
MA0003.10.902292
MA0004.10.297884
MA0006.11.55315
MA0007.10.771118
MA0009.10.724811
MA0014.10.756964
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.11.62261
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.894156
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.3329
MA0056.10
MA0057.10.542827
MA0058.10.219229
MA0059.10.218203
MA0060.11.04213
MA0061.10.923994
MA0063.10
MA0066.11.00709
MA0067.11.03434
MA0068.12.74747
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.12.68736
MA0074.10.383033
MA0076.12.66679
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.12.01936
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.489275
MA0105.11.15008
MA0106.10.424592
MA0107.10.385539
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.11.1195
MA0114.10.376635
MA0115.10.959312
MA0116.10.391626
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.0663461
MA0140.11.65424
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.11.70801
MA0146.10.886077
MA0147.10.793354
MA0148.10.319209
MA0149.10.342334
MA0062.22.46031
MA0035.20.350194
MA0039.21.01865
MA0138.21.19549
MA0002.20.0821804
MA0137.20.54754
MA0104.21.03881
MA0047.20.413608
MA0112.20.355033
MA0065.21.73813
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.481963
MA0155.10.845872
MA0156.11.05198
MA0157.10.515488
MA0158.10
MA0159.11.87789
MA0160.10.332385
MA0161.10
MA0162.11.67029
MA0163.10.390307
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.20.356906
MA0079.25.82421
MA0102.21.25596
MA0258.10.335505
MA0259.10.412624
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
CHD2#110675.569858449139857.97823784692744e-050.00122157921491754
E2F1#186972.642440346473480.007795016405580970.0320235905271997
EGR1#195883.069648673729320.001265684169336790.0084925659467629
ELF1#199792.947913971482140.0006034034679179530.00503949258583632
ETS1#211364.490197348708770.001065086822859670.00752462982430093
HDAC2#306644.127883149731160.01276819603247030.0460382401324068
HEY1#23462113.418555498012529.95779509504428e-060.000261039699279952
IRF1#365995.287267214005784.89873907841973e-060.000151411485827487
IRF3#3661310.84198897188220.002348319735717040.0133103313187101
JUND#372763.228306434709710.00591865992840790.0265466576879103
MAX#414962.978102542618670.008858766958238280.0336143279447554
MYC#460993.61542591111420.0001163729219938740.00158129997399405
NRF1#489987.514018121668251.78371877765449e-066.69866254654647e-05
PAX5#507963.078261014389770.007515152955548730.0309872106883238
POLR2A#5430132.147453176558074.83928878402115e-050.000840669463264112
POU2F2#545264.202826488188860.001513180596708150.00965689387959685
SETDB1#9869412.40616190092630.0002257725657253050.00250179957472521
SIX5#14791245.257450878602770.005466268737389780.0247567927434627
SP2#666848.04724015195220.001156447879090330.0079069237344887
TAF1#6872123.08588887914954.82574043270037e-060.000149509197582555
TBP#6908113.136498273696942.43452380190334e-050.000528056555237762
TRIM28#1015545.720161552388470.004039935478390260.0193411332306945
USF1#739162.93607658948060.009503763178720540.0357990161805668
YY1#752893.400041288360360.000191901385293490.00231485201878803
ZEB1#693579.093771086369773.17961465987139e-060.000107086673802744
ZNF143#770277.269702758891951.40394872054989e-050.000338630485971155



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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