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{{f5samples
{{f5samples
|id=FF:432-17C5
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000310,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001443,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005482,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|name=lung, embryo E15
|sample_id=432
|rna_tube_id=17C5
|rna_box=17
|rna_position=C5
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=15 days embryo
|sample_tissue=lung
|sample_donor(cell lot)=
|sample_sex=mixture
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=
|rna_concentration=
|sample_note=
|profile_hcage=CNhs11020,LSID731,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
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|comment=
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|creation_date=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:432-17C5
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011348
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011348
|name=lung, embryo E15
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=UBERON:0000310
|part_of=UBERON:0000310
|profile_cagescan=,,,
|profile_hcage=CNhs11020,LSID731,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=17
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=C5
|rna_rin=
|rna_sample_type=
|rna_tube_id=17C5
|rna_weight_ug=
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_description=
|sample_dev_stage=15 days embryo
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=432
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=lung
|top_motifs=IKZF2:1.99239853601;NKX3-1:1.95246091064;ZNF384:1.78696186364;GFI1:1.53203031987;HBP1_HMGB_SSRP1_UBTF:1.38935697567;E2F1..5:1.37494153111;STAT1,3:1.35456517513;GATA4:1.2997402143;POU1F1:1.16725471655;TOPORS:1.13878088195;FOXP1:1.12195806797;TFDP1:1.05260474632;PAX4:1.02983313789;NKX6-1,2:1.01724174466;T:1.00189421004;GZF1:0.984108996683;HOX{A5,B5}:0.97635917503;ZBTB16:0.974957282781;TEF:0.973746676381;DBP:0.965275915415;EVI1:0.9189729487;EP300:0.883956351776;NFY{A,B,C}:0.830424210031;SOX2:0.819690301646;FOXD3:0.790060940236;CDX1,2,4:0.784166726075;PITX1..3:0.765254125966;HMX1:0.757444548224;SRF:0.754395005646;TEAD1:0.721349988769;ZNF238:0.709662030722;NKX2-1,4:0.706832018273;HMGA1,2:0.660014301992;MAZ:0.605211670087;BPTF:0.602450278879;IKZF1:0.594846124858;MYBL2:0.594731327274;ZNF143:0.594445173634;RREB1:0.593764718417;MZF1:0.584449678545;SOX{8,9,10}:0.574640392716;PAX6:0.565735591659;CDC5L:0.546993104944;TLX1..3_NFIC{dimer}:0.53764775722;XCPE1{core}:0.528479664837;ALX1:0.516899701813;PATZ1:0.494956210033;SOX5:0.479920052151;NANOG{mouse}:0.468281378759;FOXL1:0.452804546571;KLF4:0.428881707143;UFEwm:0.422043107611;HIF1A:0.416389529109;POU3F1..4:0.408689052446;NKX2-2,8:0.406483271648;ZNF423:0.389635675089;NRF1:0.378495783984;FOX{I1,J2}:0.341400042203;AIRE:0.337438318305;SOX17:0.328158116521;ELF1,2,4:0.327663712487;SPIB:0.317837601657;ONECUT1,2:0.295003548499;HAND1,2:0.294351781123;BREu{core}:0.27850489479;GTF2I:0.27349325248;PAX5:0.270513192739;GTF2A1,2:0.253022421211;NANOG:0.244418233671;PRDM1:0.239349180347;FOXP3:0.211713006034;RFX2..5_RFXANK_RFXAP:0.201958701082;CRX:0.196472084299;TFCP2:0.196198746521;SPZ1:0.176681823133;HIC1:0.175009441707;ZIC1..3:0.17469735926;NKX2-3_NKX2-5:0.159060900074;NKX3-2:0.153493571703;LEF1_TCF7_TCF7L1,2:0.151674412353;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.143856847268;ALX4:0.141481763913;RXR{A,B,G}:0.134750715281;FOXQ1:0.130392681875;ELK1,4_GABP{A,B1}:0.124697546354;ADNP_IRX_SIX_ZHX:0.0933195090168;RXRA_VDR{dimer}:0.0900190323307;GATA6:0.0683438706019;MYB:0.0656653316303;MEF2{A,B,C,D}:0.0513227405029;POU6F1:0.0326517788514;PRRX1,2:0.0264219970388;POU5F1:0.0144477645932;EBF1:0.0113461696296;TBX4,5:0.0108777364031;CUX2:-0.00485791385906;MED-1{core}:-0.00574966317122;RFX1:-0.0148987372786;YY1:-0.0305173836421;NFATC1..3:-0.048692701884;GFI1B:-0.0567816003014;PAX8:-0.0578898459967;TFAP2B:-0.0627268082635;OCT4_SOX2{dimer}:-0.0648088410461;NFIX:-0.0695477431276;SP1:-0.0763389329324;FOX{D1,D2}:-0.0786199595155;ZFP161:-0.0873348990845;FOXO1,3,4:-0.105741816892;EGR1..3:-0.126081911022;ETS1,2:-0.12855239619;LHX3,4:-0.13568758186;GCM1,2:-0.135756826489;NR6A1:-0.139725206807;PBX1:-0.143888551153;HOXA9_MEIS1:-0.146059638719;GLI1..3:-0.14670631269;EN1,2:-0.15000199537;DMAP1_NCOR{1,2}_SMARC:-0.163835625696;RBPJ:-0.170506371015;AHR_ARNT_ARNT2:-0.186451798491;VSX1,2:-0.202876169805;HSF1,2:-0.217350067538;TFAP4:-0.223318968205;POU2F1..3:-0.235229905765;TBP:-0.238346602066;MTE{core}:-0.24135621891;SPI1:-0.247482330272;SNAI1..3:-0.250685587385;ATF2:-0.259528835353;RUNX1..3:-0.264075938783;ARID5B:-0.27314484462;FOXA2:-0.29652011019;HNF1A:-0.307967351891;NR3C1:-0.310733250393;bHLH_family:-0.37016570359;TFAP2{A,C}:-0.38873818163;CREB1:-0.399844378371;TLX2:-0.400446921647;HNF4A_NR2F1,2:-0.412240835013;FOXN1:-0.413739902439;PAX1,9:-0.415960730182;TP53:-0.447720290081;IRF7:-0.469569633593;JUN:-0.47922369498;NFKB1_REL_RELA:-0.48483059827;IRF1,2:-0.48799732961;MTF1:-0.498099599114;NFE2L1:-0.503706223963;TGIF1:-0.514324920581;AR:-0.5279600947;REST:-0.555659329877;ZNF148:-0.574137768376;STAT5{A,B}:-0.577446645632;ZEB1:-0.595640689803;HOX{A4,D4}:-0.618031071685;NR1H4:-0.625170336397;ESR1:-0.63651058816;MYFfamily:-0.64550415377;BACH2:-0.662008873569;NFIL3:-0.670422527875;FOS_FOS{B,L1}_JUN{B,D}:-0.683372123779;HLF:-0.688765990744;FOSL2:-0.725545313984;FOX{F1,F2,J1}:-0.754790653668;PPARG:-0.766028455268;FOXM1:-0.793272180963;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.809574997312;PDX1:-0.848167791632;NHLH1,2:-0.854594234059;ZBTB6:-0.8554550263;HES1:-0.85882085854;ESRRA:-0.860316417131;ATF4:-0.863271003783;ATF5_CREB3:-0.870677827539;CEBPA,B_DDIT3:-0.898998724601;SMAD1..7,9:-0.929002581599;LMO2:-0.935941412661;PAX2:-0.936760309744;NFE2L2:-0.986975073988;RORA:-1.00213118595;TAL1_TCF{3,4,12}:-1.0368720663;ATF6:-1.11423312518;NFE2:-1.13419378589;STAT2,4,6:-1.2537579439;NR5A1,2:-1.27368457064;SREBF1,2:-1.48759162555;MYOD1:-1.51109879756;MAFB:-1.66900620006
}}
}}

Revision as of 15:34, 21 March 2012


Name:lung, embryo E15
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
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

CNhs11020

00
10
100
1000
10000
10010.0241
10020.128
10030.0665
10040
1005-0.096
1006-0.138
10070.0915
10080
10090.15
1010.115
10100
10110
10120
1013-0.17
10140.364
10150.226
10160.21
10170
10180
10190
1020
10200
1021-0.00109
1022-0.0484
10230
10240.0956
10250.919
10260
10270.043
10280
10290.306
1030.13
10300
10310.394
1032-0.0504
10330.00159
10340
10350
10360.223
10370
10380.158
1039-0.0991
1040
10400.206
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: CNhs11020

Jaspar motifP-value
MA0002.20.0037
MA0003.10.371
MA0004.10.627
MA0006.10.897
MA0007.10.285
MA0009.10.548
MA0014.10.333
MA0017.11.14548e-4
MA0018.20.0799
MA0019.10.529
MA0024.14.34845e-9
MA0025.10.163
MA0027.10.0295
MA0028.10.11
MA0029.10.637
MA0030.10.223
MA0031.10.0104
MA0035.20.00446
MA0038.10.127
MA0039.20.0318
MA0040.10.496
MA0041.10.202
MA0042.10.302
MA0043.10.94
MA0046.12.82406e-10
MA0047.20.708
MA0048.19.5677e-4
MA0050.12.12865e-4
MA0051.14.28927e-4
MA0052.10.0575
MA0055.10.00148
MA0057.10.224
MA0058.10.548
MA0059.10.757
MA0060.12.31021e-5
MA0061.10.0852
MA0062.20.702
MA0065.22.61974e-4
MA0066.10.0181
MA0067.10.136
MA0068.10.973
MA0069.10.615
MA0070.10.351
MA0071.10.0169
MA0072.10.003
MA0073.10.592
MA0074.10.521
MA0076.10.288
MA0077.10.492
MA0078.10.529
MA0079.20.0703
MA0080.24.66735e-5
MA0081.10.575
MA0083.10.0172
MA0084.10.683
MA0087.10.693
MA0088.10.641
MA0090.10.273
MA0091.10.816
MA0092.10.626
MA0093.10.612
MA0099.21.15773e-5
MA0100.10.643
MA0101.10.5
MA0102.20.673
MA0103.10.00388
MA0104.20.842
MA0105.10.038
MA0106.10.642
MA0107.10.309
MA0108.20.0644
MA0111.10.35
MA0112.20.0052
MA0113.10.175
MA0114.18.2418e-5
MA0115.10.0501
MA0116.10.504
MA0117.10.0293
MA0119.10.507
MA0122.10.365
MA0124.10.312
MA0125.10.943
MA0131.10.256
MA0135.10.178
MA0136.13.59743e-4
MA0137.20.049
MA0138.23.63063e-6
MA0139.10.413
MA0140.10.178
MA0141.10.00101
MA0142.10.666
MA0143.10.244
MA0144.10.175
MA0145.10.118
MA0146.10.561
MA0147.10.903
MA0148.10.625
MA0149.10.0641
MA0150.14.94858e-5
MA0152.10.0685
MA0153.11.37683e-5
MA0154.10.031
MA0155.10.371
MA0156.10.234
MA0157.10.164
MA0159.10.00614
MA0160.10.0012
MA0162.10.867
MA0163.10.923
MA0164.10.942
MA0258.14.21311e-4
MA0259.10.638



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: CNhs11020

Novel motifP-value
10.248
100.715
1000.763
1010.739
1020.933
1030.702
1040.64
1050.662
1060.189
1070.644
1080.69
1090.148
110.126
1100.824
1110.0697
1120.129
1130.567
1140.0305
1150.531
1160.997
1170.822
1180.724
1190.0718
120.534
1200.148
1210.74
1220.735
1230.166
1240.846
1250.595
1260.826
1270.451
1280.147
1290.0676
130.108
1300.0253
1310.314
1320.924
1330.659
1340.459
1350.819
1360.962
1370.887
1380.762
1390.00833
140.322
1400.473
1410.46
1420.865
1430.676
1440.707
1450.968
1460.101
1470.314
1480.243
1490.338
150.138
1500.766
1510.0483
1520.177
1530.362
1540.722
1550.887
1560.335
1570.958
1580.845
1590.0208
1600.239
1610.997
1620.824
1630.0366
1640.716
1650.214
1660.158
1670.927
1680.456
1690.372
170.15
180.0752
190.708
20.378
200.476
210.408
220.495
230.0602
240.668
250.234
260.0531
270.18
280.234
290.616
30.283
300.475
310.219
320.0944
330.933
340.679
350.155
360.528
370.352
380.544
390.578
40.633
400.396
410.224
420.604
430.266
440.0222
450.198
460.52
470.261
480.145
490.191
50.461
500.539
510.654
520.569
530.655
540.24
550.544
560.355
570.968
580.282
590.251
60.755
600.307
610.862
620.0599
630.358
640.309
650.164
660.77
670.419
680.155
690.731
70.876
707.17346e-4
710.544
720.132
730.0954
740.646
750.366
760.322
770.164
780.462
790.87
80.462
800.147
810.113
820.13
830.912
840.248
850.036
860.406
870.00466
880.354
890.245
90.749
900.0383
910.69
920.065
930.979
940.774
950.366
960.387
970.187
980.204
990.993



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: CNhs11020


FANTOM5 (FF) ontology

Direct parent terms

part_of relathionship
UBERON:0000310 breast

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)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000310 (breast)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001443 (chest)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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

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