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Coexpression cluster:C1919: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;4:19.4862414338429:1.37275300118359e-05:0.000332411200302836!BCL11A#53335;4:22.6955640828856:7.49488101632307e-06:0.000214454213277744!BCL3#602;4:27.6376822429907:3.425174836939e-06:0.00011417868968882!CHD2#1106;4:8.27521826729349:0.000402837356710173:0.00387902735547241!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239408834714367!EBF1#1879;5:8.906466846569:1.78355672307702e-05:0.000406531821478483!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447412656855288!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121233847253199!IRF4#3662;4:17.5316101493953:2.08739444052064e-05:0.00046099680265074!MEF2A#4205;5:18.7432309096441:4.31877656850983e-07:2.07093069806519e-05!MEF2C#4208;4:33.0490835940992:1.68127439756556e-06:6.36428477011053e-05!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00239281825015535!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127818894144254!POU2F2#5452;5:9.10612405774252:1.59639992500654e-05:0.000370009790873854!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386824722377721!RXRA#6256;4:16.0596937113066:2.95432243260421e-05:0.000615615483916103!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00248335596019834!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194910827586761!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000575047698821904!SRF#6722;4:11.0377426097342:0.000129925581484675:0.00171070320280862!TCF12#6938;4:8.50757192174914:0.000361421557849226:0.00361314311096155!USF2#7392;4:10.3937579080557:0.000164617972868753:0.00202742175335374!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298533873470786
|tf_chipseq_enrich=BATF#10538;4:19.4862414338429:1.37275300118359e-05:0.000332411200302836!BCL11A#53335;4:22.6955640828856:7.49488101632307e-06:0.000214454213277744!BCL3#602;4:27.6376822429907:3.425174836939e-06:0.00011417868968882!CHD2#1106;4:8.27521826729349:0.000402837356710173:0.00387902735547241!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239408834714367!EBF1#1879;5:8.906466846569:1.78355672307702e-05:0.000406531821478483!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447412656855288!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121233847253199!IRF4#3662;4:17.5316101493953:2.08739444052064e-05:0.00046099680265074!MEF2A#4205;5:18.7432309096441:4.31877656850983e-07:2.07093069806519e-05!MEF2C#4208;4:33.0490835940992:1.68127439756556e-06:6.36428477011053e-05!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00239281825015535!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127818894144254!POU2F2#5452;5:9.10612405774252:1.59639992500654e-05:0.000370009790873854!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386824722377721!RXRA#6256;4:16.0596937113066:2.95432243260421e-05:0.000615615483916103!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00248335596019834!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194910827586761!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000575047698821904!SRF#6722;4:11.0377426097342:0.000129925581484675:0.00171070320280862!TCF12#6938;4:8.50757192174914:0.000361421557849226:0.00361314311096155!USF2#7392;4:10.3937579080557:0.000164617972868753:0.00202742175335374!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298533873470786
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,1.25018,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.703495,0.621241,0.778743,1.37937,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.0713,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,1.42042,0.132849,0.451846,1.25074,0.533483,0.734485,0.609718,0.124583,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,1.64902,0.659455,0.688844,1.04369,1.74665,1.55219,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,1.58259,0.189341,1.23387,0.741483,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,2.38448,1.18161,0.0719601,0.49825,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,1.49495,1.45429,0.897476,1.7218,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,1.69829,0.177807,0.126633,1.15522,3.19738,0.736459,1.56426,1.93328,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
}}
}}

Revision as of 15:11, 26 November 2012


Full id: C1919_immature_CD4_Dendritic_Peripheral_Natural_migratory_CD8



Phase1 CAGE Peaks

Hg19::chr3:135913298..135913322,-p7@MSL2
Hg19::chr3:16553385..16553420,-p@chr3:16553385..16553420
-
Hg19::chr3:16553696..16553720,+p@chr3:16553696..16553720
+
Hg19::chr3:16553730..16553747,+p@chr3:16553730..16553747
+
Hg19::chr3:16553761..16553777,+p@chr3:16553761..16553777
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
leukocyte1.27e-71136
hematopoietic cell1.35e-60177
hematopoietic stem cell8.66e-60168
angioblastic mesenchymal cell8.66e-60168
hematopoietic lineage restricted progenitor cell1.01e-56120
nongranular leukocyte6.49e-56115
hematopoietic oligopotent progenitor cell2.07e-52161
hematopoietic multipotent progenitor cell2.07e-52161
lymphoid lineage restricted progenitor cell1.93e-3952
lymphocyte1.85e-3853
common lymphoid progenitor1.85e-3853
nucleate cell1.32e-3655
classical monocyte1.30e-2142
CD14-positive, CD16-negative classical monocyte1.30e-2142
lymphocyte of B lineage8.89e-2124
pro-B cell8.89e-2124
myeloid leukocyte7.80e-2072
granulocyte monocyte progenitor cell2.46e-1967
mesenchymal cell2.30e-18354
myeloid cell5.95e-18108
common myeloid progenitor5.95e-18108
defensive cell6.58e-1848
phagocyte6.58e-1848
macrophage dendritic cell progenitor1.20e-1761
connective tissue cell1.53e-17361
myeloid lineage restricted progenitor cell1.21e-1666
monopoietic cell2.26e-1559
monocyte2.26e-1559
monoblast2.26e-1559
promonocyte2.26e-1559
T cell3.93e-1525
pro-T cell3.93e-1525
mature alpha-beta T cell6.40e-1518
alpha-beta T cell6.40e-1518
immature T cell6.40e-1518
mature T cell6.40e-1518
immature alpha-beta T cell6.40e-1518
motile cell1.13e-14386
dendritic cell2.81e-1310
B cell6.41e-1314
CD4-positive, alpha-beta T cell3.30e-126
stem cell7.25e-12441
multi fate stem cell3.16e-11427
somatic stem cell9.30e-11433
circulating cell1.15e-106
Langerhans cell2.27e-105
conventional dendritic cell5.73e-108
intermediate monocyte1.27e-089
CD14-positive, CD16-positive monocyte1.27e-089
naive T cell3.76e-073
plasmacytoid dendritic cell4.83e-073
natural killer cell5.11e-073
pro-NK cell5.11e-073
CD8-positive, alpha-beta T cell6.01e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.31e-2498
blood island2.31e-2498
hemolymphoid system6.38e-22108
immune system3.02e-1993
bone marrow4.45e-1776
connective tissue1.99e-16371
bone element4.05e-1582
skeletal element6.20e-1390
skeletal system1.58e-11100
hemopoietic organ2.52e-077
immune organ2.52e-077
Disease
Ontology termp-valuen
lymphoma6.89e-0710


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
BATF#10538419.48624143384291.37275300118359e-050.000332411200302836
BCL11A#53335422.69556408288567.49488101632307e-060.000214454213277744
BCL3#602427.63768224299073.425174836939e-060.00011417868968882
CHD2#110648.275218267293490.0004028373567101730.00387902735547241
CTCF#1066444.288205098460020.005152015588243280.0239408834714367
EBF1#187958.9064668465691.78355672307702e-050.000406531821478483
ELF1#199743.406478367046030.01235066105299550.0447412656855288
EP300#203345.419153380978560.00209386927943890.0121233847253199
IRF4#3662417.53161014939532.08739444052064e-050.00046099680265074
MEF2A#4205518.74323090964414.31877656850983e-072.07093069806519e-05
MEF2C#4208433.04908359409921.68127439756556e-066.36428477011053e-05
NFKB1#479055.488063424193840.0002008162847462320.00239281825015535
PAX5#507945.335652424942260.002223389586187790.0127818894144254
POU2F2#545259.106124057742521.59639992500654e-050.000370009790873854
RAD21#588548.284027116365060.0004011622639122450.00386824722377721
RXRA#6256416.05969371130662.95432243260421e-050.000615615483916103
SIN3A#2594255.408884726815140.0002159522671657270.00248335596019834
SP1#666744.558705102512720.00407573565781680.0194910827586761
SPI1#668858.204323508522732.68916109982495e-050.000575047698821904
SRF#6722411.03774260973420.0001299255814846750.00171070320280862
TCF12#693848.507571921749140.0003614215578492260.00361314311096155
USF2#7392410.39375790805570.0001646179728687530.00202742175335374
YY1#752843.928936599883080.007193866269917620.0298533873470786



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.