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Coexpression cluster:C2519: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346435422058143!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512252409447469!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172982285482437!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817493779573956!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.00072687051965566!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997078061838762!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240491469049894!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160918889850368!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175807432657791!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.019205956349166!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186117953347944!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248140654903433!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.0030754606463689!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466237814062163!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142397338412933!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434977647121437!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000826691015390015!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796466612514825!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.0060167596292083!SMARCC2#6601;3:70.6165308201732:4.74678670742709e-06:0.000147194078662998!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684324139619552!SREBF1#6720;4:47.0058494404883:2.04523668136926e-07:1.10274896110235e-05!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584588768220294!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507967882022681!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976780280047915
|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346435422058143!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512252409447469!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172982285482437!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817493779573956!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.00072687051965566!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997078061838762!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240491469049894!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160918889850368!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175807432657791!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.019205956349166!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186117953347944!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248140654903433!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.0030754606463689!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466237814062163!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142397338412933!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434977647121437!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000826691015390015!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796466612514825!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.0060167596292083!SMARCC2#6601;3:70.6165308201732:4.74678670742709e-06:0.000147194078662998!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684324139619552!SREBF1#6720;4:47.0058494404883:2.04523668136926e-07:1.10274896110235e-05!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584588768220294!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507967882022681!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976780280047915
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.902371,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,1.23038,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,1.34056,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,1.28263,1.32819,6.51544,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,10.0705,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,1.40954,0.717043,1.46636,1.22649,6.5812,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,1.91548,3.0147,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
}}
}}

Revision as of 15:33, 26 November 2012


Full id: C2519_cerebellum_CD8_Natural_CD4_Mast_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr1:144533782..144533805,+p@chr1:144533782..144533805
+
Hg19::chr4:2420335..2420354,-p2@ZFYVE28
Hg19::chr4:2420357..2420413,-p1@ZFYVE28
Hg19::chr4:2420416..2420440,-p4@ZFYVE28


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
leukocyte3.41e-14136
nongranular leukocyte2.24e-12115
hematopoietic lineage restricted progenitor cell1.69e-11120
defensive cell4.48e-1148
phagocyte4.48e-1148
myeloid leukocyte5.77e-1172
granulocyte monocyte progenitor cell1.51e-1067
macrophage dendritic cell progenitor6.62e-1061
classical monocyte7.36e-1042
CD14-positive, CD16-negative classical monocyte7.36e-1042
mature alpha-beta T cell8.03e-1018
alpha-beta T cell8.03e-1018
immature T cell8.03e-1018
mature T cell8.03e-1018
immature alpha-beta T cell8.03e-1018
monopoietic cell1.53e-0959
monocyte1.53e-0959
monoblast1.53e-0959
promonocyte1.53e-0959
myeloid lineage restricted progenitor cell3.30e-0966
hematopoietic cell1.33e-08177
hematopoietic stem cell4.99e-08168
angioblastic mesenchymal cell4.99e-08168
T cell1.06e-0725
pro-T cell1.06e-0725
hematopoietic oligopotent progenitor cell2.14e-07161
hematopoietic multipotent progenitor cell2.14e-07161
Uber Anatomy
Ontology termp-valuen
adult organism9.37e-29114
neural tube6.14e-2256
neural rod6.14e-2256
future spinal cord6.14e-2256
neural keel6.14e-2256
regional part of nervous system1.34e-2053
regional part of brain1.34e-2053
brain2.49e-1768
future brain2.49e-1768
regional part of forebrain3.82e-1741
forebrain3.82e-1741
anterior neural tube3.82e-1741
future forebrain3.82e-1741
neural plate5.20e-1682
presumptive neural plate5.20e-1682
central nervous system1.72e-1581
nervous system4.52e-1589
neurectoderm6.59e-1586
brain grey matter3.58e-1434
gray matter3.58e-1434
telencephalon7.11e-1434
hematopoietic system1.10e-1398
blood island1.10e-1398
hemolymphoid system1.91e-13108
cerebral hemisphere4.16e-1332
regional part of telencephalon4.35e-1332
regional part of cerebral cortex3.78e-1222
neocortex3.86e-1120
pre-chordal neural plate7.01e-1161
bone marrow1.82e-0976
cerebral cortex1.93e-0925
pallium1.93e-0925
immune system1.94e-0993
structure with developmental contribution from neural crest2.07e-09132
bone element1.31e-0882
ecto-epithelium1.17e-07104
lateral plate mesoderm1.49e-07203
tube2.75e-07192


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)

{{{tfbs_overrepresentation_jaspar}}}



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
ATF3#467316.84738089450660.0003409986823655640.00346435422058143
CCNT2#90546.336201576962630.0006203100587215640.00512252409447469
CHD2#110637.758017125587640.003351522464536340.0172982285482437
CTCF#1066445.360256373075030.001211145381643620.00817493779573956
E2F4#1874412.66806031528443.88145892637771e-050.00072687051965566
E2F6#187645.017155731697390.00157802193473060.00997078061838762
EBF1#187936.679850134926750.005184294118278910.0240491469049894
ELF1#199744.258097958807540.003041525565781240.0160918889850368
ESR1#2099323.07645247211590.0001339105244968570.00175807432657791
ETS1#211337.296570691651750.00400857377511390.019205956349166
HEY1#2346244.040111043105710.00375304636917980.0186117953347944
HMGN3#932448.178547723350590.0002234570284440470.00248140654903433
IRF1#365947.63716375356390.0002938853996185490.0030754606463689
MAX#414934.839416631755340.01315737137836840.0466237814062163
MXI1#460149.96157162875930.0001015224754950450.00142397338412933
PAX5#507935.002174148383370.01196533174786410.0434977647121437
RFX5#5993412.04791082719514.74457429336527e-050.000826691015390015
SIN3A#2594245.408884726815140.001168172384885160.00796466612514825
SIX5#147912312.81503651659420.0007664471136930380.0060167596292083
SMARCC2#6601370.61653082017324.74678670742709e-060.000147194078662998
SP1#666745.69838137814090.0009482606065333980.00684324139619552
SREBF1#6720447.00584944048832.04523668136926e-071.10274896110235e-05
SRF#6722413.79717826216782.75840773062708e-050.000584588768220294
USF1#739146.361499277207960.0006105011399140830.00507967882022681
ZNF143#7702310.12565741417090.001534861610688180.00976780280047915



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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