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{{f5samples
{{f5samples
|id=FF:1271-21F2
|ancestors_in_anatomy_facet=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002095,UBERON:0002100,UBERON:0002106,UBERON:0002193,UBERON:0002323,UBERON:0002390,UBERON:0002405,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003081,UBERON:0003104,UBERON:0003281,UBERON:0004119,UBERON:0004120,UBERON:0004177,UBERON:0004185,UBERON:0004457,UBERON:0004458,UBERON:0004782,UBERON:0004854,UBERON:0004872,UBERON:0004921,UBERON:0004923,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0005602,UBERON:0006293,UBERON:0007026,UBERON:0009034,UBERON:0009142
|name=spleen, embryo E18
|sample_id=1271
|rna_tube_id=21F2
|rna_box=21
|rna_position=F2
|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=18 days embryo
|sample_tissue=spleen
|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=CNhs11011,LSID730,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002095,UBERON:0002100,UBERON:0002106,UBERON:0002193,UBERON:0002323,UBERON:0002390,UBERON:0002405,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003081,UBERON:0003104,UBERON:0003281,UBERON:0004119,UBERON:0004120,UBERON:0004177,UBERON:0004185,UBERON:0004457,UBERON:0004458,UBERON:0004782,UBERON:0004854,UBERON:0004872,UBERON:0004921,UBERON:0004923,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0005602,UBERON:0006293,UBERON:0007026,UBERON:0009034,UBERON:0009142
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=fantom:1271-21F2
|created_by=
|creation_date=
|def=
|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=fantom:1271-21F2
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:1271-21F2
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011517
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011517
|name=spleen, embryo E18
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11011,LSID730,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=21
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=F2
|rna_rin=
|rna_sample_type=
|rna_tube_id=21F2
|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=18 days embryo
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=1271
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=spleen
|top_motifs=GATA6:2.44516528449;IRF7:1.86094369719;SPIB:1.65978599157;E2F1..5:1.40949554745;ZNF423:1.37513320101;SPI1:1.12980889226;ELF1,2,4:1.11448195914;ETS1,2:1.04288599343;IKZF2:1.033989162;NKX2-2,8:1.01655813966;ZBTB16:1.00471825663;NFE2L2:0.982905170852;GFI1:0.934358676832;CEBPA,B_DDIT3:0.932252833384;STAT5{A,B}:0.926962429471;FOXP1:0.883205395681;IRF1,2:0.870291893992;RUNX1..3:0.705692490253;HMGA1,2:0.682715959898;PBX1:0.647489002717;DMAP1_NCOR{1,2}_SMARC:0.632064583344;IKZF1:0.631599014993;AIRE:0.616817255545;MYBL2:0.614172396869;POU5F1:0.609373996734;STAT1,3:0.606133062088;NR3C1:0.597864622407;RXRA_VDR{dimer}:0.58254974148;ZNF148:0.579742540044;NKX3-1:0.489026845838;MYB:0.486094373994;PRDM1:0.479080700754;ALX4:0.476705325085;GLI1..3:0.452282571297;NKX6-1,2:0.375469260073;PAX1,9:0.372337719535;TEF:0.369551583548;ZNF238:0.34836101132;NR6A1:0.317364623436;POU1F1:0.307975707524;FOX{I1,J2}:0.265777832188;PAX4:0.248437144722;ARID5B:0.241141206015;FOXP3:0.225930109423;TBX4,5:0.225761653576;PITX1..3:0.220337698119;GZF1:0.21384743017;SPZ1:0.2032142386;HOXA9_MEIS1:0.190971228536;TAL1_TCF{3,4,12}:0.168369743211;PDX1:0.148466440766;SRF:0.145811518426;ZNF384:0.142714308517;EBF1:0.141443058504;NFE2:0.138257105718;CDX1,2,4:0.134882438719;EP300:0.134227639196;EN1,2:0.128064817703;TBP:0.121390788227;FOXO1,3,4:0.111109797766;RBPJ:0.109707585052;TEAD1:0.109377163109;XCPE1{core}:0.102037170766;SOX{8,9,10}:0.0862655270441;TLX1..3_NFIC{dimer}:0.0816974802861;MZF1:0.0640811395985;NFY{A,B,C}:0.061621746301;TOPORS:0.0553509136995;GATA4:0.0533739364058;NFIX:0.0232231949236;NFKB1_REL_RELA:0.0203012969696;RREB1:0.00578265340919;EVI1:-0.00260719345002;FOXL1:-0.00285812832225;ELK1,4_GABP{A,B1}:-0.00432592019038;HOX{A5,B5}:-0.00621483450134;FOX{D1,D2}:-0.0368820581613;TFAP4:-0.0427081012225;TFDP1:-0.049253211227;STAT2,4,6:-0.0581949539978;HLF:-0.0688357847946;SOX5:-0.0738033142238;SOX17:-0.0755376640501;FOXM1:-0.0828430912362;RXR{A,B,G}:-0.0850689979032;MTF1:-0.0943801887756;HSF1,2:-0.170358912861;OCT4_SOX2{dimer}:-0.170989203239;POU2F1..3:-0.182527891085;NKX2-1,4:-0.193540643002;GCM1,2:-0.227019809286;PATZ1:-0.229214613247;YY1:-0.22935332074;ZNF143:-0.229961146248;NFATC1..3:-0.233310040578;MAZ:-0.250822784813;PRRX1,2:-0.259420849767;GTF2I:-0.294468273414;PPARG:-0.294666676653;BACH2:-0.315035892157;NRF1:-0.333186384469;ZIC1..3:-0.334394083357;NANOG{mouse}:-0.337699076379;GFI1B:-0.343964156785;ALX1:-0.34826350061;BREu{core}:-0.355276757721;EGR1..3:-0.366487352413;NKX2-3_NKX2-5:-0.367500274476;KLF4:-0.380057466345;TLX2:-0.391397793904;PAX2:-0.397365396169;HBP1_HMGB_SSRP1_UBTF:-0.41908431019;DBP:-0.420002940525;FOX{F1,F2,J1}:-0.425123479563;NR1H4:-0.44544012362;CUX2:-0.448722252446;ATF4:-0.454918640951;LHX3,4:-0.460051404562;ATF5_CREB3:-0.463988689091;PAX6:-0.467667115413;SOX2:-0.469536342648;SMAD1..7,9:-0.481982982867;HNF1A:-0.486259807372;MEF2{A,B,C,D}:-0.486515999822;GTF2A1,2:-0.519393374131;SP1:-0.521949689506;HAND1,2:-0.529081869371;FOXA2:-0.53512411587;MYFfamily:-0.540390265658;HNF4A_NR2F1,2:-0.54249502634;FOXD3:-0.547641302457;AHR_ARNT_ARNT2:-0.568424350083;ESR1:-0.571380899511;TFAP2{A,C}:-0.591118389407;NKX3-2:-0.592219655814;ZFP161:-0.603809882404;bHLH_family:-0.615961599236;HES1:-0.644040099203;CREB1:-0.656146104642;HMX1:-0.660026480572;POU6F1:-0.665862433396;TGIF1:-0.667680056229;FOS_FOS{B,L1}_JUN{B,D}:-0.67096839025;MED-1{core}:-0.676577077469;LMO2:-0.689668416424;BPTF:-0.703048867751;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.715629881571;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.720225770648;HOX{A4,D4}:-0.740241460235;CRX:-0.746051749861;RFX1:-0.748565609937;VSX1,2:-0.750978472267;NHLH1,2:-0.755211376097;UFEwm:-0.756539165132;PAX8:-0.76017118805;TFAP2B:-0.777367790313;ONECUT1,2:-0.786495969514;RFX2..5_RFXANK_RFXAP:-0.793576977746;PAX5:-0.802050076958;MTE{core}:-0.802433238779;T:-0.805230886707;NR5A1,2:-0.843095541489;REST:-0.852041054092;RORA:-0.862092406393;MYOD1:-0.863969622797;NFE2L1:-0.898301474505;ATF2:-0.902574871824;SREBF1,2:-0.906584161442;TFCP2:-0.917638539364;SNAI1..3:-0.941382367273;HIC1:-0.9726556127;ADNP_IRX_SIX_ZHX:-1.00073230439;JUN:-1.00260519501;MAFB:-1.00426919313;TP53:-1.10324258099;CDC5L:-1.11759475013;FOXN1:-1.1219531484;NFIL3:-1.12264255188;FOSL2:-1.15428655526;NANOG:-1.18609898341;ZBTB6:-1.20974964831;HIF1A:-1.21179207746;ZEB1:-1.21534899574;ESRRA:-1.25675785965;LEF1_TCF7_TCF7L1,2:-1.35544581;POU3F1..4:-1.37919956689;AR:-1.56150201997;ATF6:-1.65764543902;FOXQ1:-1.92335058877
}}
}}

Revision as of 15:19, 21 March 2012


Name:spleen, embryo E18
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespleen
dev stage18 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

CNhs11011

00
10
100
1000
10000.0573
10010
10020.254
1003-0.0842
10040
10050.223
1006-0.143
1007-0.0247
10080
10090.0508
1010.152
10100
1011-0.0131
10120.0738
1013-0.0799
10140.192
1015-0.00719
1016-0.00909
10170
10180
10190
1020
10200
10210.0738
1022-0.246
10230.0738
10240.102
10250.192
10260
10270
10280
10290.142
1030.0738
10300.192
10310.201
1032-0.147
10330.0738
10340.0506
10350
10360.297
10370
1038-0.102
1039-0.211
1040
10400.176
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: CNhs11011

Jaspar motifP-value
MA0002.20.00172
MA0003.10.458
MA0004.10.83
MA0006.10.137
MA0007.10.658
MA0009.10.231
MA0014.10.967
MA0017.10.921
MA0018.22.51421e-7
MA0019.10.604
MA0024.16.05905e-7
MA0025.10.0017
MA0027.10.147
MA0028.10.0331
MA0029.10.808
MA0030.10.261
MA0031.10.414
MA0035.21.0515e-5
MA0038.10.429
MA0039.20.277
MA0040.10.921
MA0041.10.191
MA0042.10.542
MA0043.10.0103
MA0046.13.32153e-10
MA0047.20.898
MA0048.10.0174
MA0050.11.02382e-7
MA0051.14.73432e-5
MA0052.11.316e-5
MA0055.10.0223
MA0057.10.775
MA0058.10.906
MA0059.10.64
MA0060.10.606
MA0061.10.00334
MA0062.28.21893e-6
MA0065.20.766
MA0066.10.6
MA0067.10.155
MA0068.10.955
MA0069.10.366
MA0070.10.261
MA0071.10.43
MA0072.10.343
MA0073.10.879
MA0074.10.739
MA0076.10.0289
MA0077.10.271
MA0078.10.368
MA0079.20.139
MA0080.21.052e-13
MA0081.19.32232e-4
MA0083.10.967
MA0084.10.96
MA0087.10.0725
MA0088.10.14
MA0090.10.157
MA0091.10.207
MA0092.10.669
MA0093.10.848
MA0099.20.448
MA0100.10.848
MA0101.10.0321
MA0102.20.0195
MA0103.10.00141
MA0104.20.63
MA0105.11.11841e-5
MA0106.10.783
MA0107.10.0367
MA0108.20.144
MA0111.10.847
MA0112.20.0159
MA0113.10.385
MA0114.10.167
MA0115.10.033
MA0116.10.00403
MA0117.10.418
MA0119.10.0831
MA0122.10.57
MA0124.10.362
MA0125.10.0597
MA0131.10.99
MA0135.10.101
MA0136.15.80958e-14
MA0137.20.0453
MA0138.20.00354
MA0139.10.157
MA0140.11.73618e-30
MA0141.10.522
MA0142.10.408
MA0143.10.216
MA0144.10.24
MA0145.10.939
MA0146.10.271
MA0147.10.746
MA0148.10.694
MA0149.10.612
MA0150.10.118
MA0152.10.136
MA0153.19.01108e-7
MA0154.10.00188
MA0155.10.65
MA0156.15.98618e-19
MA0157.10.646
MA0159.10.753
MA0160.10.404
MA0162.10.308
MA0163.11.20397e-5
MA0164.10.987
MA0258.10.341
MA0259.10.91



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: CNhs11011

Novel motifP-value
10.217
100.0466
1000.995
1010.662
1020.412
1030.0439
1040.992
1050.591
1060.0614
1070.0988
1080.599
1090.0566
110.172
1100.132
1110.307
1120.0275
1130.494
1140.847
1150.488
1160.844
1170.0104
1180.241
1190.509
120.557
1200.806
1210.547
1220.724
1230.0165
1240.79
1250.0955
1260.232
1270.354
1280.0883
1290.619
130.001
1300.0594
1310.948
1320.358
1330.144
1340.188
1350.441
1360.9
1370.0233
1380.289
1390.945
140.865
1400.0684
1410.911
1420.181
1430.255
1440.222
1450.00181
1460.907
1470.605
1480.0296
1490.992
150.0825
1500.0687
1510.345
1520.701
1530.319
1540.714
1550.184
1562.71243e-20
1570.63
1580.142
1590.186
1600.0616
1610.0798
1620.645
1630.782
1640.00798
1650.124
1660.778
1670.436
1680.848
1690.0277
170.658
180.47
190.19
20.648
200.271
210.183
220.46
230.721
240.175
250.91
260.00303
270.987
280.681
290.0526
30.0215
300.631
310.977
320.961
330.13
340.516
350.697
360.316
370.109
380.757
390.694
40.695
400.25
410.609
420.0259
430.0986
440.354
450.903
460.11
470.423
480.304
490.209
50.17
500.223
510.969
520.771
530.666
540.791
550.251
560.56
570.0995
580.56
590.128
60.725
600.144
610.104
620.287
630.381
640.552
650.928
660.827
670.158
680.625
690.984
70.0106
700.751
710.00856
720.31
730.28
740.361
750.176
760.652
770.984
780.0131
790.443
80.0884
800.00974
810.614
820.364
830.917
840.00255
850.807
860.873
870.0476
880.808
890.981
90.293
900.17
910.151
920.569
930.411
940.161
950.207
960.416
970.938
980.362
990.414



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: CNhs11011


FANTOM5 (FF) ontology

Direct parent terms


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
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002095 (mesentery)
0002100 (trunk)
0002106 (spleen)
0002193 (hemolymphoid system)
0002323 (body cavity)
0002390 (hematopoietic system)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003281 (mesentery of stomach)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004782 (gastrointestinal system serosa)
0004854 (gastrointestinal system mesentery)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0005602 (dorsal mesogastrium)
0006293 (spleen primordium)
0007026 (primitive gut)
0009034 (stomach region)
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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