Personal tools

FF:976-16D8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:976-16D8 |name=intestine, embryo E15, biol_rep1 |sample_id=976 |rna_tube_id=976-16D8 |rna_box=976-16D8 |rna_position=976-16D8 |sample_cell_lot= |sam...")
 
No edit summary
Line 40: Line 40:
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|sample_description=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 66:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=GFI1:1.680843985;ZNF238:1.40382928843;GZF1:1.34783780103;MYBL2:1.18600479308;NFY{A,B,C}:1.15570200101;FOX{I1,J2}:1.09212632107;SRF:1.05548673558;MAZ:0.989245809122;NANOG:0.988745632541;PDX1:0.988689018662;E2F1..5:0.960149953916;TLX2:0.951493013826;CDX1,2,4:0.92010223409;ZNF423:0.905818828489;HNF1A:0.892285278004;ZNF143:0.838113241766;XCPE1{core}:0.837093478571;ADNP_IRX_SIX_ZHX:0.831543787064;TOPORS:0.812995214432;RREB1:0.781754113604;TFDP1:0.765567051099;EP300:0.765150421649;ZNF148:0.740988315177;PAX1,9:0.737045945326;NKX2-1,4:0.727890006025;RBPJ:0.68205409247;ATF6:0.664845440624;ZNF384:0.654924111357;SOX17:0.648013864693;HNF4A_NR2F1,2:0.64187247537;PATZ1:0.630168686759;GATA6:0.596672934777;MZF1:0.57931279474;GTF2I:0.549726638222;DBP:0.543317763228;GFI1B:0.525431368357;HBP1_HMGB_SSRP1_UBTF:0.518377915013;PBX1:0.518335730357;TEAD1:0.511683018127;SP1:0.494885644396;PRRX1,2:0.491378669123;NANOG{mouse}:0.484766783689;LHX3,4:0.477304517375;ZIC1..3:0.476175504;HMGA1,2:0.471354434932;SNAI1..3:0.468145261193;STAT1,3:0.448563282189;BREu{core}:0.443745265647;PAX6:0.434130904324;ONECUT1,2:0.433921651527;NKX3-2:0.423864918744;RXR{A,B,G}:0.397915471645;SOX{8,9,10}:0.396653216326;TFCP2:0.392816453445;LEF1_TCF7_TCF7L1,2:0.392422300798;SOX2:0.380439704595;HIC1:0.380336159506;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.373130350141;T:0.370882586022;FOXA2:0.367520484053;TLX1..3_NFIC{dimer}:0.36651996692;ZEB1:0.328642082407;HMX1:0.328052181279;CUX2:0.31544644221;HIF1A:0.313080457022;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.311080037282;SPZ1:0.29026718807;MED-1{core}:0.278717963256;AHR_ARNT_ARNT2:0.259556835983;ATF2:0.252682647894;CRX:0.249236047934;NRF1:0.248840702632;TBX4,5:0.224486292656;IKZF2:0.215173810421;OCT4_SOX2{dimer}:0.212395563713;TBP:0.212186417341;GATA4:0.200615432003;EBF1:0.190173953511;HOX{A5,B5}:0.18695314574;IKZF1:0.185284338658;VSX1,2:0.184456815715;bHLH_family:0.183278041882;FOXM1:0.182889736193;FOXQ1:0.178450250684;TFAP2B:0.173390955716;PAX8:0.170674420263;PRDM1:0.163397484754;GLI1..3:0.163198935033;POU6F1:0.155562623463;FOXD3:0.1446012295;POU3F1..4:0.14404989432;GCM1,2:0.143837487302;EN1,2:0.121456039775;NR6A1:0.121342610729;FOX{F1,F2,J1}:0.105009018402;NKX3-1:0.100245149193;HAND1,2:0.0979566862866;HSF1,2:0.0923521896963;ELF1,2,4:0.0720743754009;FOX{D1,D2}:0.0719249864844;SMAD1..7,9:0.066129615503;FOXN1:0.061612840295;ELK1,4_GABP{A,B1}:0.0528886979551;CDC5L:0.0444582665978;TFAP4:0.0426711667956;ZFP161:0.0223906519723;ETS1,2:0.0105464195885;EGR1..3:0.00110556785341;ESRRA:-0.0171291955281;FOS_FOS{B,L1}_JUN{B,D}:-0.0209038376516;GTF2A1,2:-0.0297660018334;TFAP2{A,C}:-0.0455226511356;ALX4:-0.0526857688379;PITX1..3:-0.0677885042478;MYB:-0.0738727687594;NFIX:-0.0751430649263;NKX2-3_NKX2-5:-0.0787156518043;KLF4:-0.0842320876838;MTF1:-0.0887730662655;REST:-0.0959211366121;SPIB:-0.103047361767;MTE{core}:-0.103778234951;NHLH1,2:-0.108179509952;STAT5{A,B}:-0.126902655076;FOSL2:-0.12743353554;ZBTB16:-0.128441133136;MYOD1:-0.128496138578;NFKB1_REL_RELA:-0.137129988509;JUN:-0.151031305475;EVI1:-0.165192841838;RXRA_VDR{dimer}:-0.173140262167;SOX5:-0.179700357358;DMAP1_NCOR{1,2}_SMARC:-0.180759010845;TEF:-0.192079467626;LMO2:-0.199287881289;RFX1:-0.206625043101;TGIF1:-0.207484121288;TP53:-0.215090074965;RUNX1..3:-0.220362705632;AIRE:-0.224463133354;POU2F1..3:-0.24709441402;MYFfamily:-0.256541112787;AR:-0.269833224703;ESR1:-0.27407981195;YY1:-0.279019054642;MEF2{A,B,C,D}:-0.28097727602;SPI1:-0.300092042833;PAX5:-0.305043175062;POU5F1:-0.318623682379;ARID5B:-0.32702505899;NFATC1..3:-0.333658201467;NR3C1:-0.354838855892;HOXA9_MEIS1:-0.358023620854;SREBF1,2:-0.368640189369;RFX2..5_RFXANK_RFXAP:-0.399787372842;FOXP1:-0.413251521073;ZBTB6:-0.425730607894;NKX2-2,8:-0.427131009514;ATF5_CREB3:-0.443119876879;UFEwm:-0.45073389404;FOXL1:-0.468445037327;HLF:-0.49113605636;IRF1,2:-0.495470699311;PAX2:-0.504270329828;ATF4:-0.509223258328;NR1H4:-0.54353063466;CREB1:-0.550087192009;PAX4:-0.589704075664;BACH2:-0.596475404851;MAFB:-0.615056894633;IRF7:-0.617910646688;FOXO1,3,4:-0.619712080206;STAT2,4,6:-0.621792528099;TAL1_TCF{3,4,12}:-0.656437394091;NR5A1,2:-0.659152801519;RORA:-0.67074586376;CEBPA,B_DDIT3:-0.714032502194;POU1F1:-0.718688514449;BPTF:-0.77852957579;HES1:-0.781215046833;NFE2L1:-0.815091942687;NFE2L2:-0.844354500594;NFE2:-0.853557596689;PPARG:-1.00553121349;ALX1:-1.02666965022;HOX{A4,D4}:-1.03280405436;NKX6-1,2:-1.09507768421;FOXP3:-1.24196444063;NFIL3:-1.24301256631
}}
}}

Revision as of 15:19, 15 February 2012


Name:intestine, embryo E15, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage15 days embryo
sexmixture
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]





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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs10602

00
10
100
1000
10000.0996
1001-0.00926
10020.299
1003-0.00275
10040
10050.042
1006-0.0642
10070.0652
10080
10090.0534
1010.133
10100.142
10110
10120
1013-0.12
10140.241
10150.171
10160.167
10170
10180.0195
10190
1020
10200
10210
1022-0.0704
10230
10240
10250.676
10260.0188
10270.0526
10280
10290.132
1030.142
10300
10310.416
10320.044
10330.0244
10340
10350
10360.125
10370
10380.035
1039-0.114
1040
10400.0951
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


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

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10602

Jaspar motifP-value
MA0002.29.49712e-4
MA0003.10.48
MA0004.10.938
MA0006.10.88
MA0007.10.474
MA0009.10.526
MA0014.10.532
MA0017.10.244
MA0018.20.481
MA0019.10.485
MA0024.12.0755e-7
MA0025.10.0314
MA0027.10.091
MA0028.10.726
MA0029.10.956
MA0030.10.936
MA0031.10.635
MA0035.20.0249
MA0038.10.00593
MA0039.20.197
MA0040.10.428
MA0041.10.461
MA0042.10.978
MA0043.10.679
MA0046.11.98927e-54
MA0047.20.149
MA0048.10.449
MA0050.11.52894e-4
MA0051.18.29912e-4
MA0052.10.013
MA0055.10.364
MA0057.10.547
MA0058.10.914
MA0059.10.274
MA0060.11.11012e-15
MA0061.10.272
MA0062.20.282
MA0065.20.161
MA0066.10.0453
MA0067.10.112
MA0068.10.946
MA0069.10.316
MA0070.10.716
MA0071.10.0431
MA0072.10.0762
MA0073.10.976
MA0074.10.681
MA0076.10.689
MA0077.10.152
MA0078.10.99
MA0079.20.175
MA0080.20.179
MA0081.10.116
MA0083.11.21617e-5
MA0084.10.873
MA0087.10.247
MA0088.10.975
MA0090.10.279
MA0091.10.737
MA0092.10.56
MA0093.10.917
MA0099.20.22
MA0100.10.146
MA0101.10.394
MA0102.20.939
MA0103.10.87
MA0104.20.711
MA0105.10.0376
MA0106.10.259
MA0107.10.289
MA0108.20.0235
MA0111.10.354
MA0112.20.00132
MA0113.10.711
MA0114.10.122
MA0115.10.133
MA0116.10.0572
MA0117.10.0259
MA0119.10.0549
MA0122.10.654
MA0124.10.644
MA0125.10.385
MA0131.10.178
MA0135.10.0261
MA0136.10.422
MA0137.20.496
MA0138.20.0829
MA0139.10.984
MA0140.10.261
MA0141.10.0161
MA0142.10.426
MA0143.10.893
MA0144.10.867
MA0145.10.394
MA0146.10.918
MA0147.10.444
MA0148.10.109
MA0149.10.0708
MA0150.10.00238
MA0152.10.904
MA0153.12.22914e-33
MA0154.10.0753
MA0155.10.268
MA0156.10.847
MA0157.10.419
MA0159.10.172
MA0160.10.0885
MA0162.10.894
MA0163.10.745
MA0164.10.815
MA0258.14.1904e-4
MA0259.10.717



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10602

Novel motifP-value
10.0445
100.194
1000.66
1010.577
1020.379
1030.0525
1040.849
1050.665
1060.357
1070.919
1080.987
1090.143
110.116
1100.238
1110.0212
1120.257
1130.485
1145.87304e-4
1150.207
1160.766
1170.084
1180.514
1190.0996
120.502
1200.996
1210.797
1220.817
1230.28
1240.274
1250.207
1260.504
1270.388
1280.321
1290.207
130.946
1300.319
1310.774
1320.707
1330.472
1340.901
1350.81
1360.73
1370.781
1380.061
1390.108
140.383
1400.0196
1410.545
1420.146
1430.0383
1440.323
1450.909
1460.679
1470.401
1480.759
1490.666
150.052
1500.832
1510.0663
1520.571
1530.12
1540.31
1550.348
1565.86971e-4
1570.458
1580.34
1590.203
1600.398
1610.917
1620.452
1630.291
1640.15
1650.309
1660.207
1670.341
1680.434
1690.187
170.209
180.115
190.939
20.619
200.344
210.542
220.582
230.121
240.435
250.281
260.778
270.677
280.117
290.423
30.121
300.572
310.314
320.177
330.685
340.568
350.0613
360.176
370.0571
380.527
390.867
40.883
400.891
410.197
420.323
430.121
440.114
450.606
460.392
470.237
480.215
490.0617
50.114
500.597
510.743
520.371
530.583
540.621
550.395
560.5
570.0957
580.252
590.211
60.788
600.712
610.962
620.0157
630.168
640.525
650.268
660.725
670.143
680.289
690.111
70.693
709.77315e-4
710.227
720.658
730.0711
740.958
750.0425
760.303
770.429
780.343
790.364
80.0378
800.247
810.212
820.018
830.0978
840.974
850.00643
860.793
870.948
880.538
890.427
90.936
900.0126
910.0684
920.148
930.566
940.0408
950.12
960.0873
970.826
980.161
990.483



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10602


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000061 (anatomical structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:976-16D8&oldid=413799"