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Difference between revisions of "FF:3139-67G5"

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|creation_date=
 
|creation_date=
 
|def=
 
|def=
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|expression_enrichment_score=chr13:83643159..83643226,+!p3@Mef2c!1.57!35.78!Mef2c;;chr6:55631042..55631102,-!p1@Neurod6!1.47!28.45!Neurod6;;chr3:99057269..99057306,+!p1@Tbx15!1.46!33.56!Tbx15;;chr1:136186574..136186592,+!p1@Myog!1.38!23.11!Myog;;chr2:120365588..120365602,-!p2@Zfp106!1.35!35.56!Zfp106;;chr7:6649134..6649167,-!p1@Zim1!1.33!106.90!Zim1;;chr12:34642510..34642530,+!p1@Twist1!1.32!61.56!Twist1;;chr4:87452180..87452196,-!p3@Mllt3!1.31!38.00!Mllt3;;chr10:106931775..106931798,-!p1@Myf6!1.25!16.67!Myf6;;chr9:74709695..74709722,+!p1@Onecut1!1.25!16.67!Onecut1;;chr4:87452200..87452229,-!p2@Mllt3!1.24!34.45!Mllt3;;chr12:74147689..74147711,-!p1@Six1!1.20!32.45!Six1;;chr10:22539932..22539956,-!p1@Tcf21!1.18!37.56!Tcf21;;chr15:103085660..103085681,-!p1@Nfe2!1.15!19.56!Nfe2;;chr12:30213247..30213333,+!p1@Myt1l!1.15!13.11!Myt1l;;chr7:53631837..53631850,+!p1@Myod1!1.12!12.22!Myod1;;chr12:37835141..37835194,+!p1@Meox2!1.11!37.12!Meox2;;chr7:119885539..119885574,+!p3@Tead1!1.11!12.00!Tead1;;chr10:88969376..88969395,-!p1@Nr1h4!1.11!11.78!Nr1h4;;chr3:3634145..3634161,+!p1@Hnf4g!1.08!11.11!Hnf4g;;chr9:91260616..91260653,-!p2@Zic1!1.08!10.89!Zic1;;chr7:17647736..17647772,-!p1@Hif3a!1.06!37.12!Hif3a;;chr13:72766250..72766273,+!p1@Irx2!1.04!15.56!Irx2;;chr10:80555320..80555378,-!p1@Creb3l3!1.04!11.56!Creb3l3;;chr11:96143666..96143725,+!p1@Hoxb8!1.04!11.56!Hoxb8;;chr8:87425854..87425891,+!p1@Klf1!1.04!10.00!Klf1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.03!12.22!Pou3f3;;chr1:169548377..169548430,+!p1@Rxrg!1.03!9.78!Rxrg;;chr15:102828658..102828678,+!p1@Hoxc6!1.03!9.78!Hoxc6;;chr2:79296783..79296801,-!p1@Neurod1!1.03!9.78!Neurod1;;chr10:12810631..12810649,+!p1@Plagl1!1.02!250.69!Plagl1;;chr5:77543897..77543911,-!p2@Hopx!1.02!18.22!Hopx;;chr15:102197405..102197454,-!p1@Sp7!1.00!8.89!Sp7;;chr1:179374784..179374800,+!p2@Zfp238!0.99!10.45!Zfp238;;chr11:85699862..85699920,+!p1@Tbx4!0.99!8.67!Tbx4;;chr16:91270004..91270023,+!p1@Olig1!0.98!9.78!Olig1;;chr2:65683890..65683907,+!p1@Csrnp3!0.97!16.45!Csrnp3;;chr12:37835120..37835133,+!p2@Meox2!0.97!12.00!Meox2;;chr12:30219426..30219506,+!p2@Myt1l!0.96!8.22!Myt1l;;chr16:25801993..25802014,+!p1@Trp63!0.96!8.22!Trp63;;chr11:98190918..98190951,-!p1@Neurod2!0.96!8.22!Neurod2;;chr7:116154364..116154444,+!p1@Tub!0.95!14.00!Tub;;chr3:95032091..95032183,-!p1@Mllt11!0.92!65.56!Mllt11;;chr15:85566184..85566238,+!p1@Ppara!0.92!11.11!Ppara;;chr11:94981424..94981439,+!p1@Dlx3!0.90!8.00!Dlx3;;chr17:44951553..44951586,-!p2@Runx2!0.90!7.78!Runx2;;chr2:32229906..32229942,+!p3@Ciz1!0.90!6.89!Ciz1;;chr11:121380640..121380655,-!p1@Zfp750!0.89!11.56!Zfp750;;chr2:103143336..103143367,-!p1@Ehf!0.89!11.33!Ehf;;chr2:71384802..71384815,-!p1@Dlx2!0.89!8.45!Dlx2;;chr2:28477452..28477483,-!p1@Gfi1b!0.88!8.22!Gfi1b;;chr7:122989594..122989626,-!p1@Sox6!0.88!6.67!Sox6;;chr1:137155026..137155042,-!p1@Elf3!0.87!39.78!Elf3;;chr10:126778916..126778974,-!p1@Gli1!0.87!15.11!Gli1;;chr14:67853425..67853454,+!p1@Ebf2!0.87!9.33!Ebf2;;chr2:38206580..38206600,+!p2@Lhx2!0.87!8.00!Lhx2;;chr2:38206744..38206766,+!p1@Lhx2!0.87!7.78!Lhx2;;chr13:40829137..40829205,-!p1@Tfap2a!0.87!7.33!Tfap2a;;chr5:148118639..148118715,-!p1@Cdx2!0.87!6.45!Cdx2;;chr9:91260594..91260612,-!p1@Zic1!0.87!6.45!Zic1;;chr19:19185671..19185693,-!p1@Rorb!0.86!15.78!Rorb;;chr13:83643232..83643254,+!p5@Mef2c!0.86!6.22!Mef2c;;chr11:101755669..101755686,-!p1@Meox1!0.85!11.33!Meox1;;chrX:90531838..90531861,+!p1@Arx!0.85!7.78!Arx;;chr17:44951431..44951445,-!p3@Runx2!0.85!6.00!Runx2;;chr6:52190467..52190500,-!p1@Hoxa10!0.85!6.00!Hoxa10;;chr17:48015839..48015915,-!p3@Foxp4!0.83!6.89!Foxp4;;chr16:25684232..25684285,+!p2@Trp63!0.83!5.78!Trp63;;chr12:37835248..37835260,+!p4@Meox2!0.83!5.78!Meox2;;chr7:122989632..122989668,-!p2@Sox6!0.83!5.78!Sox6;;chr3:99057677..99057730,+!p2@Tbx15!0.83!5.78!Tbx15;;chr1:57029281..57029326,-!p1@Satb2!0.82!9.11!Satb2;;chr14:67853457..67853482,+!p2@Ebf2!0.82!8.22!Ebf2;;chr10:106923133..106923146,-!p1@Myf5!0.82!5.56!Myf5;;chr15:85566537..85566552,+!p2@Ppara!0.82!5.56!Ppara;;chr13:55932591..55932622,-!p1@Pitx1!0.81!6.67!Pitx1;;chr16:38294860..38294924,-!p1@Nr1i2!0.80!5.33!Nr1i2;;chr12:28027561..28027591,-!p1@Sox11!0.79!37.12!Sox11;;chr8:59799772..59799789,+!p1@Hand2!0.79!16.00!Hand2;;chr1:57028125..57028149,-!p2@Satb2!0.79!5.11!Satb2;;chr2:61642631..61642684,+!p1@Tbr1!0.79!5.11!Tbr1;;chr6:6831928..6831949,-!p3@Dlx5!0.79!5.11!Dlx5;;chr12:109242266..109242295,-!p1@Bcl11b!0.78!45.56!Bcl11b;;chr19:25746898..25746910,+!p1@Dmrt2!0.78!7.78!Dmrt2;;chr14:67853632..67853674,+!p3@Ebf2!0.78!6.22!Ebf2;;chr9:31720843..31720888,-!p1@Barx2!0.77!5.56!Barx2;;chr9:96159147..96159204,+!p2@Tfdp2!0.76!9.33!Tfdp2;;chr1:165243591..165243625,-!p2@Prrx1!0.76!7.56!Prrx1;;chr6:52176164..52176195,-!p1@Hoxa9!0.76!6.00!Hoxa9;;chr10:86956396..86956411,-!p1@Ascl1!0.75!7.56!Ascl1;;chr19:59533221..59533271,+!p1@Emx2!0.75!5.78!Emx2;;chr9:43013917..43013968,-!p1@Pou2f3!0.75!4.67!Pou2f3;;chr12:37835203..37835218,+!p3@Meox2!0.74!5.56!Meox2;;chr12:54349410..54349461,+!p1@Npas3!0.74!5.56!Npas3;;chr15:76352832..76352900,-!p1@Scrt1!0.74!4.44!Scrt1;;chr15:102196745..102196769,-!p2@Sp7!0.74!4.44!Sp7;;chr4:87452167..87452178,-!p8@Mllt3!0.74!4.44!Mllt3;;chr6:115372058..115372085,+!p3@Pparg!0.74!4.44!Pparg;;chrX:108009761..108009788,+!p1@Pou3f4!0.74!4.44!Pou3f4;;chr11:44430989..44431015,+!p4@Ebf1!0.73!8.22!Ebf1;;chr1:140739014..140739032,-!p1@Lhx9!0.73!5.78!Lhx9;;chr2:74549968..74549996,+!p1@Hoxd3!0.73!5.56!Hoxd3;;chr9:96159225..96159249,+!p5@Tfdp2!0.73!4.89!Tfdp2;;chr1:165243379..165243402,-!p3@Prrx1!0.72!6.67!Prrx1;;chr13:72766279..72766296,+!p2@Irx2!0.72!6.67!Irx2;;chr6:128250380..128250442,-!p2@Tead4!0.72!5.56!Tead4;;chr15:103085690..103085710,-!p3@Nfe2!0.72!4.67!Nfe2;;chr15:103082088..103082136,-!p2@Nfe2!0.72!4.22!Nfe2;;chr10:106931839..106931851,-!p3@Myf6!0.72!4.22!Myf6;;chr6:6832076..6832092,-!p1@Dlx5!0.71!4.89!Dlx5;;chr18:80909801..80909819,-!p1@Nfatc1!0.70!26.89!Nfatc1;;chr5:98609885..98609900,+!p1@Prdm8!0.70!4.00!Prdm8;;chr3:99057256..99057268,+!p3@Tbx15!0.70!4.00!Tbx15;;chr4:154335024..154335039,+!p1@Hes5!0.69!4.89!Hes5;;chr2:180069370..180069409,-!p1@Gata5!0.69!4.67!Gata5;;chr7:35904304..35904320,+!p1@Cebpa!0.68!88.45!Cebpa;;chr2:163372884..163372904,+!p1@Hnf4a!0.68!3.78!Hnf4a;;chr17:27865882..27865901,-!p1@Spdef!0.68!3.78!Spdef;;chr3:101814061..101814094,+!p1@Nhlh2!0.68!3.78!Nhlh2;;chr10:106931803..106931817,-!p2@Myf6!0.68!3.78!Myf6;;chr12:57796615..57796687,+!p1@Pax9!0.68!3.78!Pax9;;chr4:150482563..150482655,-!p2@Camta1!0.66!14.45!Camta1;;chr4:139388835..139388867,-!p1@Pax7!0.66!3.56!Pax7;;chr16:43247391..43247422,+!p12@Zbtb20!0.66!3.56!Zbtb20;;chr1:19199236..19199258,+!p1@Tfap2b!0.66!3.56!Tfap2b;;chr19:55969923..55969944,+!p6@Tcf7l2!0.66!3.56!Tcf7l2;;chr11:83664365..83664383,+!p1@Hnf1b!0.66!3.56!Hnf1b;;chr5:135582751..135582788,+!p1@Mlxipl!0.65!15.78!Mlxipl;;chr15:35225845..35225867,+!p1@Osr2!0.65!9.78!Osr2;;chr9:87626083..87626108,-!p1@Tbx18!0.64!8.22!Tbx18;;chr4:13670499..13670526,+!p2@Runx1t1!0.64!8.22!Runx1t1;;chr7:144505980..144506010,-!p3@Ebf3!0.64!4.22!Ebf3;;chr6:6831950..6831985,-!p2@Dlx5!0.64!3.78!Dlx5;;chr17:14011485..14011507,+!p2@Mllt4!0.64!3.33!Mllt4;;chr16:91225808..91225824,+!p1@Olig2!0.64!3.33!Olig2;;chr14:122874619..122874634,+!p1@Zic2!0.64!3.33!Zic2;;chr1:57028556..57028583,-!p5@Satb2!0.64!3.33!Satb2;;chr13:99124189..99124205,+!p1@Foxd1!0.63!5.33!Foxd1;;chr4:135129538..135129558,-!p1@Grhl3!0.63!5.33!Grhl3;;chr14:99697871..99697934,+!p1@Klf5!0.61!73.56!Klf5;;chr3:5218629..5218684,+!p1@Zfhx4!0.61!11.56!Zfhx4;;chr10:44178521..44178557,-!p1@Prdm1!0.61!6.00!Prdm1;;chr8:123608252..123608268,+!p1@Foxf1a!0.61!4.89!Foxf1a;;chr13:53568104..53568156,-!p1@Msx2!0.61!4.89!Msx2;;chr16:18587076..18587106,-!p1@Tbx1!0.61!4.67!Tbx1;;chr6:52154414..52154462,-!p1@Hoxa5!0.61!4.44!Hoxa5;;chr10:88996336..88996380,-!p2@Nr1h4!0.61!4.00!Nr1h4;;chr6:52184901..52184959,-!p2@Hoxa10!0.61!3.11!Hoxa10;;chr15:50714356..50714368,-!p14@Trps1!0.61!3.11!Trps1;;chr17:25707623..25707639,-!p1@Sox8!0.60!14.89!Sox8;;chr13:31717548..31717596,+!p1@Foxf2!0.60!6.67!Foxf2;;chr1:93698030..93698064,+!p1@Twist2!0.60!6.67!Twist2;;chr1:189821714..189821761,+!p1@Esrrg!0.60!6.22!Esrrg;;chr12:58646974..58647003,-!p1@Foxa1!0.60!4.22!Foxa1;;chr9:71743854..71743909,-!p1@Tcf12!0.59!28.00!Tcf12;;chr15:76287876..76287894,+!p1@Scx!0.59!18.89!Scx;;chr2:91864300..91864379,-!p2@Creb3l1!0.59!9.56!Creb3l1;;chr4:114732112..114732158,+!p1@Tal1!0.59!7.11!Tal1;;chr11:116196664..116196679,-!p1@Foxj1!0.59!4.89!Foxj1;;chr11:96153767..96153822,+!p1@Hoxb6!0.59!4.89!Hoxb6;;chr7:30088977..30089002,+!p2@Dpf1!0.59!4.22!Dpf1;;chr10:88996295..88996335,-!p3@Nr1h4!0.59!3.56!Nr1h4;;chr18:52775562..52775650,+!p1@Zfp474!0.59!2.89!Zfp474;;chr7:108966820..108966835,+!p1@Phox2a!0.59!2.89!Phox2a;;chr7:53631818..53631829,+!p2@Myod1!0.59!2.89!Myod1;;chr8:12395603..12395621,+!p1@Sox1!0.59!2.89!Sox1;;chr2:103264213..103264233,+!p1@Elf5!0.59!2.89!Elf5;;chr1:179374820..179374831,+!p3@Zfp238!0.59!2.89!Zfp238;;chr1:165243792..165243808,-!p1@Prrx1!0.58!11.56!Prrx1;;chr2:146047829..146047847,+!p1@Insm1!0.58!5.56!Insm1;;chr14:63864056..63864102,-!p1@Gata4!0.58!5.33!Gata4;;chr1:14746065..14746079,-!p1@Msc!0.58!3.56!Msc;;chr4:82151274..82151290,-!p3@Nfib!0.57!54.01!Nfib;;chr11:44431687..44431706,+!p2@Ebf1!0.57!15.34!Ebf1;;chr2:9800207..9800234,-!p1@Gata3!0.57!9.78!Gata3;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.57!5.33!Zfhx3;;chr13:72101178..72101203,-!p1@Irx1!0.57!4.67!Irx1;;chr11:11584970..11585030,+!p2@Ikzf1!0.57!4.22!Ikzf1;;chr2:168427252..168427273,-!p2@Nfatc2!0.57!3.56!Nfatc2;;chr7:144505957..144505972,-!p2@Ebf3!0.57!3.56!Ebf3;;chr4:13670571..13670625,+!p1@Runx1t1!0.56!8.45!Runx1t1;;chr14:56443806..56443848,+!p1@Nfatc4!0.56!6.00!Nfatc4;;chr6:52163319..52163342,-!p1@Hoxa3!0.56!4.22!Hoxa3;;chr6:52167459..52167492,-!p1@Hoxa7!0.56!3.33!Hoxa7;;chr7:17642177..17642223,-!p3@Hif3a!0.56!2.67!Hif3a;;chr4:22415443..22415506,-!p1@Pou3f2!0.56!2.67!Pou3f2;;chr11:21901608..21901634,-!p1@Otx1!0.56!2.67!Otx1;;chr9:24578720..24578735,-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|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
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Revision as of 10:05, 14 May 2012


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17.5 days embryo
sexunknown_sex_type
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data

MULTIPLE



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: MULTIPLEThis sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: MULTIPLEThis sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: MULTIPLE


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA