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{{f5samples
{{f5samples
|id=FF:824-19H1
|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, neonate N20
|sample_id=824
|rna_tube_id=19H1
|rna_box=19
|rna_position=H1
|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=20 days neonate
|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=CNhs11112,LSID734,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=
|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=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:824-19H1
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011430
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011430
|name=spleen, neonate N20
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11112,LSID734,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=19
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=H1
|rna_rin=
|rna_sample_type=
|rna_tube_id=19H1
|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=20 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=824
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=spleen
|top_motifs=GATA6:3.45502805535;POU1F1:2.65689748377;PITX1..3:2.19374033841;AIRE:2.08531798932;E2F1..5:2.02224775106;ZBTB16:1.86468647682;POU2F1..3:1.77141481567;SPIB:1.741758101;POU5F1:1.7229255559;IRF1,2:1.70839228102;ALX4:1.65611680089;ARID5B:1.62942253799;STAT5{A,B}:1.51163855849;TEF:1.42672139948;ELF1,2,4:1.24182256816;FOXP1:1.23487316209;IRF7:1.21779477142;SPI1:1.19208820712;FOX{I1,J2}:1.14066499529;DMAP1_NCOR{1,2}_SMARC:1.1231321961;PBX1:1.12060451658;NR6A1:1.1156913591;ETS1,2:1.0711795771;NFY{A,B,C}:1.03772723516;MYB:1.03602051503;NFE2L2:1.01850483417;PAX1,9:1.00971076661;RUNX1..3:0.998049198324;YY1:0.952849784497;PDX1:0.938605108464;HOX{A5,B5}:0.800807365916;NFKB1_REL_RELA:0.781795857342;IKZF2:0.731210271545;CDX1,2,4:0.716815645595;OCT4_SOX2{dimer}:0.595267003877;FOXO1,3,4:0.572393975373;NKX2-2,8:0.563278795635;CEBPA,B_DDIT3:0.492298627751;GFI1:0.485879065825;ZNF423:0.461178509652;RXRA_VDR{dimer}:0.438295326224;FOXP3:0.4293264827;PPARG:0.399409070933;TFDP1:0.350556835406;NFE2:0.328330275374;TBX4,5:0.289249439043;ELK1,4_GABP{A,B1}:0.273611082678;BPTF:0.258104586183;ZNF143:0.155302845975;FOXM1:0.153134397501;ATF5_CREB3:0.139844083681;NKX6-1,2:0.137740502013;NFATC1..3:0.0967611414081;PRDM1:0.0797309462492;EVI1:0.0679459303418;NKX3-1:0.0583907011166;TAL1_TCF{3,4,12}:0.0214858092987;STAT2,4,6:0.00641239497574;FOXQ1:0.00318645882178;ZNF384:-0.07385348721;STAT1,3:-0.131758420539;LMO2:-0.144678402026;TOPORS:-0.156278645193;HES1:-0.190765929352;ATF4:-0.197529430113;SOX17:-0.199568267866;PAX8:-0.206829844232;SREBF1,2:-0.219471159845;EBF1:-0.223007706999;NRF1:-0.234373882092;PAX4:-0.244067531564;NKX3-2:-0.2509186733;GATA4:-0.258573862556;NFIX:-0.278896384356;ALX1:-0.312765644146;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.320715373224;ZNF148:-0.334461073505;TLX2:-0.33930808543;FOX{F1,F2,J1}:-0.347719254745;SRF:-0.357321336517;bHLH_family:-0.371917285055;NR1H4:-0.380558712619;HOXA9_MEIS1:-0.387182931888;SMAD1..7,9:-0.391908523027;NKX2-1,4:-0.39791414465;FOXA2:-0.404799335647;PAX6:-0.408787499819;NFE2L1:-0.4252652327;HMGA1,2:-0.443225706377;SOX{8,9,10}:-0.471694482384;RFX2..5_RFXANK_RFXAP:-0.499073927972;FOXD3:-0.515548568237;NR3C1:-0.52071045407;NANOG{mouse}:-0.535167271496;RBPJ:-0.541659559638;SPZ1:-0.541754995765;PRRX1,2:-0.546519511317;FOX{D1,D2}:-0.55159086071;TBP:-0.555767377387;UFEwm:-0.56714756271;BACH2:-0.569147294222;KLF4:-0.584733653653;BREu{core}:-0.601395330117;GLI1..3:-0.615891822509;ZFP161:-0.629909865592;FOXL1:-0.647928564885;HNF4A_NR2F1,2:-0.655539158279;EN1,2:-0.665291076506;NFIL3:-0.671581637438;CRX:-0.681971051968;MYFfamily:-0.688274002191;MEF2{A,B,C,D}:-0.694683097436;AHR_ARNT_ARNT2:-0.697902262148;HNF1A:-0.704160589009;FOS_FOS{B,L1}_JUN{B,D}:-0.729056048478;SNAI1..3:-0.735360610473;HLF:-0.744552384995;HAND1,2:-0.744991364519;RREB1:-0.750635669825;MTF1:-0.768681309339;NHLH1,2:-0.777434048913;GZF1:-0.807151193948;TLX1..3_NFIC{dimer}:-0.817280690814;CREB1:-0.832136139344;TEAD1:-0.841069152333;MZF1:-0.85584365623;RFX1:-0.856945799841;TGIF1:-0.858503163239;ZIC1..3:-0.862125295795;RORA:-0.865440156217;ATF2:-0.866289212404;EP300:-0.87741578413;TFAP4:-0.898009353819;ZEB1:-0.900323344636;MYBL2:-0.9025842864;NR5A1,2:-0.91268144702;XCPE1{core}:-0.915570662242;CUX2:-0.917704420753;NANOG:-0.937954614918;MAFB:-0.955963592426;MTE{core}:-0.958318702414;EGR1..3:-0.961109333517;MYOD1:-0.96435005961;SOX2:-1.00330661509;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.03290086511;LHX3,4:-1.05088821502;ZBTB6:-1.05761322562;MED-1{core}:-1.08942370709;POU6F1:-1.10000597315;ESR1:-1.10285546031;IKZF1:-1.10738350663;REST:-1.11218848679;HBP1_HMGB_SSRP1_UBTF:-1.11505530465;GCM1,2:-1.12460614764;PAX2:-1.13891365015;HMX1:-1.15688557097;CDC5L:-1.18206108084;JUN:-1.18288893035;HSF1,2:-1.19798144648;PATZ1:-1.20692593109;VSX1,2:-1.22677310674;ZNF238:-1.23595140906;ESRRA:-1.24293614914;GTF2I:-1.24370589691;RXR{A,B,G}:-1.26038041773;HOX{A4,D4}:-1.27776474039;GTF2A1,2:-1.28538498271;DBP:-1.2859249789;T:-1.31632259665;ONECUT1,2:-1.31771305734;TFAP2B:-1.32921368841;MAZ:-1.34337373831;TFAP2{A,C}:-1.39286497546;SP1:-1.43371162056;NKX2-3_NKX2-5:-1.46363137028;SOX5:-1.46523043154;POU3F1..4:-1.52888256456;ADNP_IRX_SIX_ZHX:-1.55459648517;HIC1:-1.55541322502;TP53:-1.58104493586;GFI1B:-1.63832956664;TFCP2:-1.68056229547;LEF1_TCF7_TCF7L1,2:-1.78100406655;FOXN1:-1.80890378639;AR:-1.82924076537;HIF1A:-1.95037413897;PAX5:-1.9728834528;ATF6:-1.97496711705;FOSL2:-2.1710028741
}}
}}

Revision as of 15:37, 21 March 2012


Name:spleen, neonate N20
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 stage20 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

CNhs11112

00
10
100
1000
10000
1001-0.00222
1002-0.0921
1003-0.0518
10040
10050.0556
1006-0.143
1007-0.00166
10080
1009-0.134
1010.133
10100
10110
10120.189
1013-0.132
1014-0.0317
1015-0.162
1016-0.324
10170
10180
10190
1020
10200
10210
1022-0.162
10230
1024-0.0761
10250
10260
10270
10280
10290.138
103-0.0447
10300.741
1031-0.317
1032-0.466
10330.00822
10340
10350
10360.25
10370
1038-0.272
1039-0.224
1040
1040-0.111
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: CNhs11112

Jaspar motifP-value
MA0002.20.00166
MA0003.10.496
MA0004.10.649
MA0006.10.38
MA0007.10.721
MA0009.10.406
MA0014.10.874
MA0017.10.252
MA0018.20.00832
MA0019.10.199
MA0024.14.57593e-6
MA0025.10.0565
MA0027.10.574
MA0028.10.0198
MA0029.10.829
MA0030.10.296
MA0031.10.593
MA0035.27.35339e-10
MA0038.10.11
MA0039.20.876
MA0040.10.617
MA0041.10.312
MA0042.10.969
MA0043.10.00276
MA0046.11.02928e-10
MA0047.20.912
MA0048.10.241
MA0050.11.02224e-10
MA0051.13.46315e-6
MA0052.14.63807e-6
MA0055.10.301
MA0057.10.816
MA0058.10.803
MA0059.10.145
MA0060.10.239
MA0061.18.72507e-4
MA0062.25.71053e-6
MA0065.20.314
MA0066.10.0829
MA0067.10.753
MA0068.10.736
MA0069.10.505
MA0070.10.226
MA0071.10.732
MA0072.10.633
MA0073.11
MA0074.10.735
MA0076.10.0402
MA0077.10.126
MA0078.10.719
MA0079.20.0259
MA0080.24.13609e-11
MA0081.10.0344
MA0083.10.0731
MA0084.10.228
MA0087.10.12
MA0088.10.111
MA0090.10.0473
MA0091.10.0543
MA0092.10.743
MA0093.10.729
MA0099.20.542
MA0100.10.069
MA0101.10.00311
MA0102.20.775
MA0103.10.881
MA0104.20.6
MA0105.15.73848e-6
MA0106.10.225
MA0107.10.00423
MA0108.25.93542e-4
MA0111.10.615
MA0112.20.00355
MA0113.10.5
MA0114.10.911
MA0115.10.669
MA0116.10.00123
MA0117.10.857
MA0119.10.235
MA0122.10.936
MA0124.10.844
MA0125.10.0529
MA0131.10.782
MA0135.10.0896
MA0136.12.41342e-13
MA0137.20.683
MA0138.20.00358
MA0139.10.231
MA0140.11.92838e-36
MA0141.10.492
MA0142.10.0778
MA0143.10.239
MA0144.10.734
MA0145.10.88
MA0146.10.313
MA0147.10.482
MA0148.10.551
MA0149.10.0523
MA0150.10.0682
MA0152.10.922
MA0153.12.30367e-7
MA0154.10.00404
MA0155.10.615
MA0156.12.51498e-11
MA0157.10.536
MA0159.10.151
MA0160.10.91
MA0162.10.261
MA0163.11.45769e-4
MA0164.10.381
MA0258.10.116
MA0259.10.909



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: CNhs11112

Novel motifP-value
10.0958
100.0174
1000.738
1010.767
1020.716
1030.01
1040.918
1050.548
1060.289
1070.657
1080.342
1090.111
110.225
1100.0806
1110.02
1120.0337
1130.898
1140.396
1150.559
1160.951
1175.90501e-4
1180.0681
1190.187
120.972
1200.992
1210.28
1220.757
1230.193
1240.974
1250.0198
1260.194
1270.38
1280.288
1290.114
130.00663
1300.532
1310.843
1320.123
1330.495
1340.0981
1350.983
1360.931
1370.0403
1380.701
1390.584
140.734
1400.232
1410.671
1420.181
1430.343
1440.961
1450.0144
1460.948
1470.88
1480.172
1490.423
150.0388
1500.189
1510.269
1520.442
1530.441
1540.27
1550.13
1560.187
1570.703
1580.0386
1590.126
1600.608
1610.091
1620.704
1630.579
1640.0286
1650.327
1660.37
1670.1
1680.477
1690.0536
170.472
180.209
190.414
20.261
200.0597
210.386
220.564
230.818
240.4
250.318
260.00187
270.758
280.19
290.0245
30.0527
300.329
310.889
320.667
330.27
340.945
350.47
360.0582
370.157
380.496
390.951
40.894
400.274
410.762
420.0747
430.109
440.474
450.706
460.147
470.169
480.237
490.051
50.0776
500.982
510.834
520.938
530.972
540.947
550.326
560.649
570.133
580.31
590.512
60.358
600.402
610.385
620.115
630.421
640.655
650.579
660.654
670.555
680.504
690.525
70.04
700.353
710.019
720.33
730.403
740.774
750.039
760.178
770.672
780.0261
790.957
80.0257
800.0284
810.436
820.569
830.462
840.16
850.323
860.584
870.772
880.587
890.652
90.46
900.0157
910.24
920.561
930.359
940.0593
950.17
960.0341
970.869
980.164
990.6



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: CNhs11112


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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