Personal tools

FF:688-20B8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:688-20B8 |name=intestine, neonate N06, biol_rep1 |sample_id=688 |rna_tube_id=688-20B8 |rna_box=688-20B8 |rna_position=688-20B8 |sample_cell_lot= |sa...")
 
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=CDX1,2,4:2.65794917663;HNF4A_NR2F1,2:2.3312881256;FOXM1:2.08901985922;DMAP1_NCOR{1,2}_SMARC:1.97037617025;HNF1A:1.78296907656;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.6484692723;RXRA_VDR{dimer}:1.64717644559;SNAI1..3:1.64575752982;NR6A1:1.51992567484;GZF1:1.23867238946;IRF1,2:1.16476590559;PDX1:1.08448831481;EVI1:1.00064657853;POU1F1:0.97734040224;FOXP1:0.960906679073;ZEB1:0.957296870438;ESRRA:0.929514086461;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.901168370188;TAL1_TCF{3,4,12}:0.881634303364;SREBF1,2:0.874593041484;XCPE1{core}:0.824399868285;ATF6:0.783190208094;MYBL2:0.765906947159;TLX1..3_NFIC{dimer}:0.762391146482;TBX4,5:0.75874054611;MYOD1:0.716640369902;NR1H4:0.705536868327;FOSL2:0.675731747674;TP53:0.663066586107;ZNF423:0.654170150146;SRF:0.653705601722;ARID5B:0.644057971086;FOXA2:0.640732130309;SP1:0.610501536323;TOPORS:0.49842076427;NFIX:0.489385345588;ZNF148:0.488030848355;EN1,2:0.477911379499;TLX2:0.472664005509;NKX2-2,8:0.411820042758;FOX{D1,D2}:0.406873923624;STAT1,3:0.402589258344;TBP:0.39449444022;GATA6:0.390173661011;STAT2,4,6:0.355238404019;BPTF:0.340215606859;ESR1:0.340042516503;EBF1:0.287411231832;NKX2-1,4:0.285677080217;ADNP_IRX_SIX_ZHX:0.280842783403;TFAP4:0.258890192168;MAZ:0.258716763199;FOX{I1,J2}:0.257841162274;LMO2:0.243668512996;T:0.241627911434;IRF7:0.22208576307;RBPJ:0.203936611819;DBP:0.16979567726;AR:0.167034542863;TEAD1:0.163452770389;IKZF2:0.161717031329;POU6F1:0.142406242715;ONECUT1,2:0.133680161248;ETS1,2:0.124069942164;GFI1:0.108168343512;FOXD3:0.106702687512;GTF2A1,2:0.104448753494;FOXO1,3,4:0.0711354355655;ELF1,2,4:0.0695059587563;HAND1,2:0.0659073206121;PAX4:0.0652822412045;NKX6-1,2:0.0609091673824;FOS_FOS{B,L1}_JUN{B,D}:0.0525383460171;LEF1_TCF7_TCF7L1,2:0.0455832869886;NANOG:-0.00945653739955;ZBTB6:-0.011884637825;REST:-0.0222458966239;SPI1:-0.0223204342219;PAX6:-0.0304550020016;FOX{F1,F2,J1}:-0.0340613486274;CEBPA,B_DDIT3:-0.0354852185629;GTF2I:-0.0371266950052;CDC5L:-0.0728118664146;ZNF238:-0.0743723441273;MYFfamily:-0.0747431308243;NKX3-1:-0.0771501990616;FOXQ1:-0.0802262923674;GCM1,2:-0.0932683699915;ZNF384:-0.117677698637;GATA4:-0.131790560924;HIF1A:-0.150067280847;CUX2:-0.154727406061;GLI1..3:-0.161742060841;AIRE:-0.168265588535;PITX1..3:-0.173766327717;TFCP2:-0.178827592173;LHX3,4:-0.190703760365;JUN:-0.20549281869;FOXL1:-0.208223731384;TEF:-0.221198277344;IKZF1:-0.22487848334;E2F1..5:-0.229089723673;PBX1:-0.2350616041;MTE{core}:-0.23993872704;HBP1_HMGB_SSRP1_UBTF:-0.248790391915;RREB1:-0.270792670279;HOXA9_MEIS1:-0.286119828448;TFAP2B:-0.29280795553;SPIB:-0.32497866071;UFEwm:-0.325054394677;NKX3-2:-0.325264691797;bHLH_family:-0.341322766174;HES1:-0.346121640921;NFKB1_REL_RELA:-0.34755275508;NFIL3:-0.362173707449;PATZ1:-0.374214618352;HIC1:-0.384262958158;PRDM1:-0.399282609193;YY1:-0.402025551626;SPZ1:-0.405088974282;NR5A1,2:-0.411562182138;GFI1B:-0.411784121645;HMX1:-0.413759654208;NKX2-3_NKX2-5:-0.427345425352;OCT4_SOX2{dimer}:-0.428927484967;NANOG{mouse}:-0.429991757281;NFY{A,B,C}:-0.438923987399;MED-1{core}:-0.443865912188;NR3C1:-0.455870053741;FOXP3:-0.463798475783;RUNX1..3:-0.484435550764;ATF5_CREB3:-0.492062622789;TFAP2{A,C}:-0.503614385461;ATF2:-0.510312872038;MTF1:-0.528538653662;KLF4:-0.531145034473;ZBTB16:-0.534995680028;CREB1:-0.536497453257;BACH2:-0.536878881504;PAX2:-0.539220042528;PAX5:-0.54398293376;HMGA1,2:-0.545036570183;BREu{core}:-0.546934676108;SOX5:-0.56717143732;PRRX1,2:-0.575030931485;MYB:-0.583168534152;EGR1..3:-0.586510848146;FOXN1:-0.606000169184;VSX1,2:-0.606139195037;HSF1,2:-0.616565703594;ZFP161:-0.617832829966;MAFB:-0.620251658207;ZIC1..3:-0.626590604058;ELK1,4_GABP{A,B1}:-0.628329001079;SMAD1..7,9:-0.632563595705;POU5F1:-0.637266314799;PAX1,9:-0.645830393253;ALX1:-0.648008886184;POU3F1..4:-0.658389299938;PAX8:-0.66284073999;ALX4:-0.678484217654;STAT5{A,B}:-0.692527119071;NFE2:-0.692739850748;NHLH1,2:-0.699667397649;TGIF1:-0.726822614862;TFDP1:-0.748160005329;RFX1:-0.753949105347;MEF2{A,B,C,D}:-0.760913925569;EP300:-0.783308826099;HLF:-0.789407184443;POU2F1..3:-0.797489896787;MZF1:-0.806560912551;SOX17:-0.813129595969;CRX:-0.824622763186;NFE2L2:-0.850671763792;SOX2:-0.87383584222;NFATC1..3:-0.892432222074;RFX2..5_RFXANK_RFXAP:-0.906493200881;AHR_ARNT_ARNT2:-0.988713890582;PPARG:-1.06587415306;SOX{8,9,10}:-1.07362821211;ATF4:-1.19037004256;RXR{A,B,G}:-1.20983897526;RORA:-1.22350030097;ZNF143:-1.26965819132;NRF1:-1.28401067704;NFE2L1:-1.32137005859;HOX{A4,D4}:-1.63622865855;HOX{A5,B5}:-1.75283026579
}}
}}

Revision as of 15:19, 15 February 2012


Name:intestine, neonate N06, 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 stage6 days neonate
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

CNhs11102

00
10
100
1000
10000.103
10010.0397
10020.271
10030.00838
10040
10050.302
10060.0644
10070.0133
10080.353
10090.12
101-0.077
10100.0974
10110
10120
10130.224
10140.177
1015-0.126
1016-0.0806
10170
10180.399
10190
1020
10200
10210.0487
10220.0251
10230
10240.0974
10250.592
10260
10270
10280
10290.515
1030.149
10300
10310.0721
10320.292
1033-0.0665
10340.0974
10350.177
1036-0.00598
10370
10380.0926
10390.00248
1040.0974
1040-0.0865
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: CNhs11102

Jaspar motifP-value
MA0002.20.394
MA0003.10.126
MA0004.10.632
MA0006.10.0483
MA0007.10.532
MA0009.10.636
MA0014.10.623
MA0017.17.72128e-26
MA0018.21.8503e-4
MA0019.10.341
MA0024.10.0291
MA0025.10.0453
MA0027.10.15
MA0028.10.131
MA0029.10.892
MA0030.10.631
MA0031.10.234
MA0035.21.5562e-5
MA0038.10.536
MA0039.28.60781e-4
MA0040.10.493
MA0041.10.272
MA0042.10.801
MA0043.15.05974e-4
MA0046.16.68208e-73
MA0047.21.55354e-4
MA0048.10.367
MA0050.13.62317e-5
MA0051.10.00278
MA0052.13.08707e-6
MA0055.10.214
MA0057.10.126
MA0058.10.411
MA0059.10.644
MA0060.10.00322
MA0061.10.516
MA0062.20.0289
MA0065.21.17264e-11
MA0066.10.216
MA0067.10.175
MA0068.10.182
MA0069.10.0268
MA0070.10.227
MA0071.10.99
MA0072.10.616
MA0073.10.777
MA0074.10.196
MA0076.10.0389
MA0077.10.0967
MA0078.10.237
MA0079.20.732
MA0080.20.061
MA0081.10.0223
MA0083.10.606
MA0084.10.86
MA0087.10.396
MA0088.10.95
MA0090.10.637
MA0091.10.997
MA0092.10.153
MA0093.10.581
MA0099.20.177
MA0100.10.0108
MA0101.10.545
MA0102.20.754
MA0103.11.48839e-5
MA0104.20.169
MA0105.10.252
MA0106.10.688
MA0107.10.52
MA0108.20.17
MA0111.10.825
MA0112.21.16896e-4
MA0113.10.554
MA0114.17.43193e-31
MA0115.16.91523e-8
MA0116.10.217
MA0117.10.679
MA0119.10.0397
MA0122.10.642
MA0124.10.203
MA0125.10.591
MA0131.10.483
MA0135.10.239
MA0136.10.714
MA0137.20.756
MA0138.20.578
MA0139.10.00983
MA0140.10.0371
MA0141.10.00528
MA0142.10.108
MA0143.10.121
MA0144.10.0622
MA0145.10.0188
MA0146.10.157
MA0147.10.137
MA0148.15.90408e-6
MA0149.10.0368
MA0150.10.967
MA0152.10.88
MA0153.11.0532e-47
MA0154.10.0111
MA0155.10.043
MA0156.10.593
MA0157.10.534
MA0159.10.00438
MA0160.10.1
MA0162.10.254
MA0163.10.0023
MA0164.10.916
MA0258.10.0637
MA0259.10.141



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: CNhs11102

Novel motifP-value
10.311
100.184
1000.689
1010.906
1020.444
1030.1
1040.807
1050.587
1060.0116
1070.00778
1080.616
1090.0904
110.26
1100.346
1110.15
1120.0167
1130.35
1140.163
1150.769
1160.27
1170.678
1180.4
1190.248
120.854
1200.792
1210.883
1220.772
1230.167
1240.858
1250.947
1260.0754
1270.613
1280.0442
1290.485
130.00186
1300.487
1310.171
1320.173
1330.718
1340.384
1350.935
1360.435
1370.53
1380.0137
1390.0771
140.596
1400.857
1410.309
1420.995
1430.183
1440.594
1450.102
1460.231
1470.598
1480.0481
1490.283
150.173
1500.24
1510.544
1520.0361
1530.267
1540.669
1550.722
1560.442
1570.397
1580.61
1590.0978
1600.0477
1610.344
1620.553
1630.0455
1640.102
1650.428
1660.685
1670.821
1680.313
1690.013
170.0836
180.971
190.0563
20.0911
200.5
210.93
220.295
230.244
240.936
250.849
260.00495
270.539
280.813
290.609
30.286
300.359
310.51
320.0116
330.206
340.486
350.776
360.969
370.0586
380.462
390.0946
40.375
400.444
410.391
420.824
430.151
440.789
450.277
460.401
470.466
480.358
490.206
50.422
500.457
510.59
520.0266
530.721
540.656
550.276
560.38
570.687
580.525
590.148
60.724
600.0336
610.371
620.68
630.259
640.623
650.274
660.3
670.445
680.365
690.847
70.106
700.278
710.074
720.887
730.211
740.857
750.332
760.49
770.0638
780.106
790.645
80.321
800.552
810.566
820.173
830.921
840.994
850.0791
860.358
870.981
880.944
890.27
90.546
900.355
910.397
920.172
930.941
940.245
950.461
960.879
970.401
980.939
990.032



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: CNhs11102


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:688-20B8&oldid=413805"