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Coexpression cluster:C1738: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:13.4779047156053:0.000824108855140936:0.00627280116041573!BATF#10538;4:19.4862414338429:1.37275300118359e-05:0.000332103198264103!BCL11A#53335;4:22.6955640828856:7.49488101632307e-06:0.000214336768473101!BCL3#602;3:20.728261682243:0.000232000521768923:0.00255024760478102!BCLAF1#9774;3:12.9915885660731:0.000917803240254255:0.00667603096593635!BHLHE40#8553;3:26.9230881281864:0.000106941952374384:0.00148938666009179!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319533367690408!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00577022565900551!FOS#2353;3:5.39877318533664:0.0115389531727874:0.0421885779944949!FOSL1#8061;3:23.8281478298238:0.000153592764366073:0.00195813900361673!FOSL2#2355;3:10.158120362737:0.00188199070341543:0.0110909167742921!FOXA1#3169;3:6.64885184963127:0.00638902516656872:0.0278072761865007!FOXA2#3170;3:14.7782782515991:0.000628919285119448:0.00517357445010948!HDAC2#3066;3:8.04937214197576:0.00369167399224669:0.0186249330987031!HNF4A#3172;3:13.8793742177722:0.000756140884743427:0.00594479056471836!HNF4G#3174;3:17.2520535158681:0.000398850377282242:0.00389522485066206!JUN#3725;3:7.5076975154018:0.00451120655290603:0.0213361969558442!JUNB#3726;3:18.3663795958927:0.000331631981170089:0.00337806617394158!MEF2A#4205;5:18.7432309096441:4.31877656850983e-07:2.06998029388985e-05!MEF2C#4208;3:24.7868126955744:0.00013665133163952:0.00178642238391537!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222033460384128!NR3C1#2908;3:8.98381399870382:0.00268799578894045:0.0147955935596686!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542459723547521!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318919134984682!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356943086972744!RXRA#6256;3:12.04477028348:0.00114526216283683:0.0078345473914008!SIRT6#51548;3:92.183042394015:2.72385929271434e-06:9.43852490616431e-05!SMARCB1#6598;3:10.9516294686944:0.00151187284834318:0.00965267688031016!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146365022276349!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194812703142667!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000574342118823349!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918432661973578!TCF12#6938;3:6.38067894131185:0.00718516865325884:0.0298291461214652!TCF7L2#6934;3:6.46210593788241:0.00693010875568919:0.0293191942127288!TRIM28#10155;3:11.1543150271575:0.00143315927152925:0.00920131070014406
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,1.16078,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,1.02276,0.287891,0.167776,0.500405,1.25808,0.645033,0.44943,0.549618,3.13094,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,1.0713,0.757784,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.218848,0.533483,0.734485,0.609718,1.85968,0.458489,0.817229,0.746838,1.67994,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,1.05625,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.963115,0.228496,0.844289,6.16227,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.780629,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,2.32322,0.437618,2.20213,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,1.80194,1.43285,2.59164,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,1.69829,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,1.35505,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 15:04, 26 November 2012


Full id: C1738_CD19_CD14_Basophils_CD34_Mast_Peripheral_Dendritic



Phase1 CAGE Peaks

Hg19::chr15:40391052..40391084,-p@chr15:40391052..40391084
-
Hg19::chr15:40391166..40391171,+p@chr15:40391166..40391171
+
Hg19::chr15:40391226..40391245,+p@chr15:40391226..40391245
+
Hg19::chr6:14729941..14729960,-p@chr6:14729941..14729960
-
Hg19::chr6:32995875..32995899,+p@chr6:32995875..32995899
+


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
leukocyte5.48e-86136
classical monocyte6.79e-7442
CD14-positive, CD16-negative classical monocyte6.79e-7442
hematopoietic lineage restricted progenitor cell1.03e-72120
nongranular leukocyte3.67e-72115
hematopoietic stem cell9.54e-69168
angioblastic mesenchymal cell9.54e-69168
hematopoietic cell4.92e-64177
defensive cell7.32e-6348
phagocyte7.32e-6348
hematopoietic oligopotent progenitor cell6.30e-61161
hematopoietic multipotent progenitor cell6.30e-61161
myeloid leukocyte4.44e-5572
granulocyte monocyte progenitor cell2.69e-5467
myeloid lineage restricted progenitor cell5.96e-5366
macrophage dendritic cell progenitor3.87e-5061
monopoietic cell7.44e-5059
monocyte7.44e-5059
monoblast7.44e-5059
promonocyte7.44e-5059
myeloid cell3.00e-39108
common myeloid progenitor3.00e-39108
stuff accumulating cell5.73e-3087
mesenchymal cell1.01e-21354
connective tissue cell7.66e-21361
lymphocyte of B lineage3.04e-2024
pro-B cell3.04e-2024
motile cell3.82e-19386
lymphoid lineage restricted progenitor cell5.31e-1952
lymphocyte1.73e-1853
common lymphoid progenitor1.73e-1853
B cell1.25e-1714
nucleate cell1.60e-1755
intermediate monocyte6.16e-179
CD14-positive, CD16-positive monocyte6.16e-179
stem cell9.43e-15441
somatic stem cell1.01e-14433
multi fate stem cell1.21e-14427
basophil3.87e-073
dendritic cell6.91e-0710
Uber Anatomy
Ontology termp-valuen
bone marrow2.61e-4876
hematopoietic system4.91e-4898
blood island4.91e-4898
immune system4.70e-4793
bone element1.14e-4382
hemolymphoid system1.22e-43108
skeletal element1.89e-3890
skeletal system4.18e-33100
connective tissue1.21e-19371
lateral plate mesoderm6.80e-18203
musculoskeletal system6.29e-15167
mesoderm1.94e-07315
mesoderm-derived structure1.94e-07315
presumptive mesoderm1.94e-07315


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#467313.47790471560530.0008241088551409360.00627280116041573
BATF#10538419.48624143384291.37275300118359e-050.000332103198264103
BCL11A#53335422.69556408288567.49488101632307e-060.000214336768473101
BCL3#602320.7282616822430.0002320005217689230.00255024760478102
BCLAF1#9774312.99158856607310.0009178032402542550.00667603096593635
BHLHE40#8553326.92308812818640.0001069419523743840.00148938666009179
CHD2#110636.206413700470110.007774550126275590.0319533367690408
EBF1#187947.12517347725520.0007230531046774210.00577022565900551
FOS#235335.398773185336640.01153895317278740.0421885779944949
FOSL1#8061323.82814782982380.0001535927643660730.00195813900361673
FOSL2#2355310.1581203627370.001881990703415430.0110909167742921
FOXA1#316936.648851849631270.006389025166568720.0278072761865007
FOXA2#3170314.77827825159910.0006289192851194480.00517357445010948
HDAC2#306638.049372141975760.003691673992246690.0186249330987031
HNF4A#3172313.87937421777220.0007561408847434270.00594479056471836
HNF4G#3174317.25205351586810.0003988503772822420.00389522485066206
JUN#372537.50769751540180.004511206552906030.0213361969558442
JUNB#3726318.36637959589270.0003316319811700890.00337806617394158
MEF2A#4205518.74323090964414.31877656850983e-072.06998029388985e-05
MEF2C#4208324.78681269557440.000136651331639520.00178642238391537
NFKB1#479044.390450739355070.004707732692524960.0222033460384128
NR3C1#290838.983813998703820.002687995788940450.0147955935596686
POU2F2#545247.284899246194020.0006631223288743860.00542459723547521
RAD21#588536.21302033727380.007751055068811640.0318919134984682
REST#597835.790017229676810.009468788694433940.0356943086972744
RXRA#6256312.044770283480.001145262162836830.0078345473914008
SIRT6#51548392.1830423940152.72385929271434e-069.43852490616431e-05
SMARCB1#6598310.95162946869440.001511872848343180.00965267688031016
SMC3#912639.02695970695970.002650964449467550.0146365022276349
SP1#666744.558705102512720.00407573565781680.0194812703142667
SPI1#668858.204323508522732.68916109982495e-050.000574342118823349
TBP#690853.706770687096390.001428755106721120.00918432661973578
TCF12#693836.380678941311850.007185168653258840.0298291461214652
TCF7L2#693436.462105937882410.006930108755689190.0293191942127288
TRIM28#10155311.15431502715750.001433159271529250.00920131070014406



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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