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Coexpression cluster:C2829: Difference between revisions

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{{Coexpression_clusters
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2.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.327251,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2829_pineal_cerebellum_occipital_thalamus_medial_globus_parietal
|id=C2829
}}

Latest revision as of 12:13, 17 September 2013


Full id: C2829_pineal_cerebellum_occipital_thalamus_medial_globus_parietal



Phase1 CAGE Peaks

Hg19::chr5:77656342..77656362,+p2@SCAMP1
Hg19::chr5:77656368..77656380,+p5@SCAMP1
Hg19::chr5:77656382..77656393,+p6@SCAMP1
Hg19::chr5:77656394..77656413,+p3@SCAMP1


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

No GOStat results

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
adult organism2.83e-27114
nervous system3.71e-2789
central nervous system6.68e-2681
neural tube3.69e-2556
neural rod3.69e-2556
future spinal cord3.69e-2556
neural keel3.69e-2556
regional part of nervous system1.84e-2353
regional part of brain1.84e-2353
brain1.09e-2268
future brain1.09e-2268
regional part of forebrain5.68e-2241
forebrain5.68e-2241
anterior neural tube5.68e-2241
future forebrain5.68e-2241
organ system subdivision5.38e-18223
brain grey matter5.90e-1834
gray matter5.90e-1834
telencephalon1.24e-1734
cerebral hemisphere6.46e-1732
regional part of telencephalon9.46e-1732
neural plate1.93e-1682
presumptive neural plate1.93e-1682
neurectoderm9.71e-1686
pre-chordal neural plate7.29e-1561
regional part of cerebral cortex1.95e-1422
ectoderm-derived structure1.11e-13171
ectoderm1.11e-13171
presumptive ectoderm1.11e-13171
cerebral cortex1.62e-1325
pallium1.62e-1325
neocortex2.76e-1320
organ7.58e-12503
structure with developmental contribution from neural crest2.33e-11132
ecto-epithelium2.52e-10104
embryo8.01e-10592
multi-cellular organism2.62e-09656
anatomical group5.91e-08625
embryonic structure5.97e-08564
developing anatomical structure6.17e-08581
anatomical system6.36e-08624
anatomical cluster8.66e-08373
germ layer2.00e-07560
germ layer / neural crest2.00e-07560
embryonic tissue2.00e-07560
presumptive structure2.00e-07560
germ layer / neural crest derived structure2.00e-07560
epiblast (generic)2.00e-07560


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)
MA0003.14.74396
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.12.80362
MA0051.11.91805
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.14.04391
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BCL11A#53335428.36945510360711.542446414682e-065.90295203748529e-05
BCL3#602434.54710280373837.01262157705428e-073.15278168267745e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141779132375584
CCNT2#90546.336201576962630.0006203100587215640.00513348353588126
CHD2#1106410.34402283411698.73193255208051e-050.001293185342891
CTCF#1066445.360256373075030.001211145381643620.00819400223576332
E2F1#186944.907389214879320.001724022357361790.0106762627323159
E2F6#187645.017155731697390.00157802193473060.0099883050206866
EBF1#187948.9064668465690.00015887907472010.00199965915698874
EGR1#195844.988179094810140.001615011500076050.0101620789285723
ELF1#199744.258097958807540.003041525565781240.016122107727992
ETS1#211349.728760922202340.0001115955317418140.00154759337930996
FOSL1#8061439.7135797163734.01511434669553e-071.93956765612643e-05
GABPB1#255347.067683836182170.0004006876864423170.00390805204373824
HDAC2#3066413.41562023662633.0859005065161e-050.000627997589633739
HEY1#2346244.040111043105710.00375304636917980.0186516492862607
HMGN3#932448.178547723350590.0002234570284440470.00248537045725962
IRF4#3662421.91451268674414.33289161192893e-060.000136631300440292
JUND#372746.994663941871030.000417684217818580.00392359435372861
MAX#414946.452555509007120.0005767613195645490.00486208535426604
MEF2A#4205418.74323090964418.0978922767748e-060.000224631015005068
MEF2C#4208441.31135449262413.42889182145094e-071.69962046958004e-05
MXI1#460149.96157162875930.0001015224754950450.00142703981402786
MYC#460945.22228187160940.001344309395272740.00889497775803911
NFKB1#479045.488063424193840.001102199566301980.00769109510957522
NR3C1#2908414.9730233311731.98868032687801e-050.000444174047602251
NRF1#4899412.21027944771094.49717228915276e-050.000795394033373116
PAX5#507946.669565531177830.0005052774169483260.00444796595993478
POU2F2#545249.106124057742520.000145395665174930.00188703589849689
RAD21#5885410.35503389545638.6948481184721e-050.00129818619391724
REST#597849.650028716128020.0001152825614219170.00157426718519137
RXRA#6256420.07461713913336.1537798808435e-060.000182531842367343
SIN3A#2594245.408884726815140.001168172384885160.00797820793258049
SMC3#9126415.04493284493281.95092670935632e-050.000439311846913464
SP1#666745.69838137814090.0009482606065333980.00685555790431549
SPI1#668848.204323508522730.000220661881527680.00249817953873923
SRF#6722413.79717826216782.75840773062708e-050.000585420331190736
STAT1#6772420.70658749719925.43610708103893e-060.000165570600010681
STAT2#6773465.26377118644075.50053512607993e-083.46693052524237e-06
TAF1#687243.343046285745290.008005664898701650.0323156818442199
TAF7#6879411.43306940492395.85061525419808e-050.000971743649066783
TBP#690843.706770687096390.005296377814784350.0244918486871048
TCF12#6938410.63446490218647.8163066689251e-050.00120242635468533
TCF7L2#6934410.77017656313737.42969445082454e-050.00115709791045282
TFAP2A#7020416.5186343730451.34240829060362e-050.00032711101134473
TFAP2C#7022410.80922860986027.32289634782688e-050.00114782526139981
USF1#739146.361499277207960.0006105011399140830.00508859764975953
YY1#752844.911170749853860.00171871838055440.0107024343517005
ZBTB33#10009431.66472502998129.93721537730495e-074.20515736138716e-05
ZBTB7A#5134147.35190930787590.000342223540015990.00347206958380901
ZNF263#1012748.221841637010680.0002187871180958320.00249807672754024



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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