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{{f5samples
{{f5samples
|id=FF:627-43G1
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000349,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0001954,UBERON:0002050,UBERON:0002346,UBERON:0002421,UBERON:0002532,UBERON:0002600,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003022,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|name=hippocampus, neonate N00
|sample_id=627
|rna_tube_id=43G1
|rna_box=43
|rna_position=G1
|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=0 day neonate
|sample_tissue=hippocampus
|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=
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|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
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|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
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|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:627-43G1
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011391
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011391
|name=hippocampus, neonate N00
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=UBERON:0002421
|part_of=UBERON:0002421
|profile_cagescan=,,,
|profile_hcage=CNhs11228,LSID748,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=43
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=G1
|rna_rin=
|rna_sample_type=
|rna_tube_id=43G1
|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=0 day neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=627
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=hippocampus
|top_motifs=LHX3,4:3.36997734407;SOX2:2.50389362775;PRRX1,2:2.41446964505;NKX6-1,2:2.37939753387;PRDM1:2.33127732565;FOXD3:2.27664142745;ZFP161:2.23185081196;BREu{core}:2.21281575791;CUX2:2.15185193179;TFDP1:2.08454643646;OCT4_SOX2{dimer}:2.08182984276;POU1F1:2.05821086975;MZF1:1.97243512402;NRF1:1.89549289582;MED-1{core}:1.89176507067;ZNF384:1.82290623655;RFX1:1.78436742451;EGR1..3:1.72745697829;AHR_ARNT_ARNT2:1.66915477744;MTE{core}:1.66237205129;TFAP2B:1.62354751443;NR3C1:1.61640075176;ZBTB6:1.55501123264;PAX8:1.54551965806;ZIC1..3:1.53200144714;POU6F1:1.49783351794;ONECUT1,2:1.49079325641;FOXQ1:1.46662035458;KLF4:1.46237148306;RFX2..5_RFXANK_RFXAP:1.42451428232;POU5F1:1.39157028955;LEF1_TCF7_TCF7L1,2:1.37877047258;REST:1.3562023788;RREB1:1.33557607452;HMGA1,2:1.29423420961;NHLH1,2:1.28641501575;PATZ1:1.27529054552;ATF5_CREB3:1.26631018819;UFEwm:1.25568980903;DBP:1.24430243634;GFI1B:1.23422166386;RBPJ:1.23017884828;HIC1:1.20585813211;EN1,2:1.18569775151;SOX{8,9,10}:1.1729625748;GTF2I:1.16452998086;CREB1:1.1479742227;MYFfamily:1.13188509011;CDX1,2,4:1.0960507215;EP300:1.09392813559;HAND1,2:1.05600897012;ZNF143:1.04531078958;NANOG:1.04375060082;IKZF2:1.01888613574;ATF2:1.01526778995;NKX2-3_NKX2-5:1.01169192003;POU3F1..4:0.99751986816;VSX1,2:0.982322447691;HBP1_HMGB_SSRP1_UBTF:0.960758269049;MAZ:0.952121586245;GATA4:0.945812997084;HSF1,2:0.923092555784;HES1:0.921787856436;ADNP_IRX_SIX_ZHX:0.882106056411;HOXA9_MEIS1:0.842337170107;MTF1:0.827412226356;FOXN1:0.79306563294;PAX4:0.792632450215;STAT1,3:0.736187530225;SMAD1..7,9:0.713613705384;MAFB:0.707829563402;TAL1_TCF{3,4,12}:0.695509311324;PAX5:0.677163068359;BPTF:0.667664873954;JUN:0.645067528699;ZBTB16:0.6153126231;LMO2:0.598101847102;SOX17:0.582625091458;SOX5:0.517338786974;NKX3-1:0.48992661121;EVI1:0.486820569309;PAX6:0.484005540258;NANOG{mouse}:0.47555875988;CDC5L:0.452606090353;HOX{A5,B5}:0.442764768921;HIF1A:0.408636198032;YY1:0.408141902094;NKX3-2:0.401686641237;HMX1:0.399687148194;FOX{F1,F2,J1}:0.369898445271;FOXP3:0.331683967517;PITX1..3:0.326415870271;NKX2-1,4:0.323948015285;TLX1..3_NFIC{dimer}:0.320772533469;ELK1,4_GABP{A,B1}:0.311710367172;SP1:0.302140471153;FOXP1:0.292727226763;CRX:0.276823115808;NFY{A,B,C}:0.255280119537;AIRE:0.248413442108;GZF1:0.244259654284;RORA:0.228698044704;bHLH_family:0.183697616461;FOXM1:0.176305997877;ATF4:0.136727377109;TGIF1:0.0626612500301;HOX{A4,D4}:0.0445083304604;TFAP2{A,C}:0.0102492120696;MYB:-0.0302690378229;XCPE1{core}:-0.053840362961;POU2F1..3:-0.0802245134263;NFIL3:-0.0880661333746;ALX1:-0.0987292927537;GCM1,2:-0.12858576658;ARID5B:-0.138777641616;PBX1:-0.145414457414;TEF:-0.160332859956;MYBL2:-0.176489852259;FOX{I1,J2}:-0.221218324214;EBF1:-0.221662067084;MYOD1:-0.245898772198;ZNF423:-0.250609360248;TFAP4:-0.260045965537;T:-0.295474021645;FOXA2:-0.321103313621;SPZ1:-0.351450458657;GFI1:-0.368495726786;AR:-0.380957280813;GTF2A1,2:-0.386983039779;E2F1..5:-0.418733750425;NFIX:-0.422163060474;FOXL1:-0.452438983198;IKZF1:-0.476472543412;CEBPA,B_DDIT3:-0.47725964863;PPARG:-0.48534829207;SREBF1,2:-0.488096532014;ZNF148:-0.515811733929;ATF6:-0.544257173431;SPIB:-0.544465450501;TOPORS:-0.545609097169;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.557004804435;IRF1,2:-0.589874526065;NFE2L1:-0.629729916837;FOX{D1,D2}:-0.654171972565;NFE2:-0.699289682305;TFCP2:-0.702585533974;MEF2{A,B,C,D}:-0.708639782432;ZEB1:-0.724443798798;SPI1:-0.73953367516;NFATC1..3:-0.7569676403;GATA6:-0.760188556162;RUNX1..3:-0.773371227486;TEAD1:-0.774410841052;DMAP1_NCOR{1,2}_SMARC:-0.776916300507;HNF1A:-0.781193624825;HNF4A_NR2F1,2:-0.790643813758;SNAI1..3:-0.806463768597;ZNF238:-0.824244668261;PAX2:-0.831286480168;TBX4,5:-0.855187260926;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.859589244574;RXR{A,B,G}:-0.861840159422;NFE2L2:-0.870949947066;HLF:-0.884959639075;NR5A1,2:-0.887597030777;NKX2-2,8:-0.88766697096;ESRRA:-0.931133112859;TLX2:-0.943647706207;STAT2,4,6:-0.95788289574;IRF7:-0.959109269309;NFKB1_REL_RELA:-1.01703047717;ELF1,2,4:-1.06301402324;FOXO1,3,4:-1.11301237026;TP53:-1.13100879777;ESR1:-1.14351170272;TBP:-1.16820960593;ETS1,2:-1.19865246571;PAX1,9:-1.22727401907;FOS_FOS{B,L1}_JUN{B,D}:-1.23707794642;NR1H4:-1.27882562896;GLI1..3:-1.28291704052;BACH2:-1.2868855541;STAT5{A,B}:-1.37498211531;RXRA_VDR{dimer}:-1.43226331869;FOSL2:-1.43718352241;NR6A1:-1.53290876056;PDX1:-1.64743853965;SRF:-1.81457241978;ALX4:-2.08966271301
}}
}}

Revision as of 15:36, 21 March 2012


Name:hippocampus, neonate N00
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuehippocampus
dev stage0 day 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

CNhs11228

00
10.423
100
1000.369
1000-0.0142
10010.0441
10020.139
10030.729
10040.0425
10050
10060.267
10070.121
10080
1009-0.19
1010.0323
10100
10110.335
10120.285
1013-0.031
1014-0.0133
10150.274
10160.262
10170
10180
10190
1020
10200
10210.04
1022-0.0704
10230
1024-0.0583
10250.0425
10260
10270.568
10280
10290.131
103-0.0754
10300
1031-0.275
1032-0.0953
10330.0425
10340
10350
1036-0.106
10370
10380.0666
1039-0.127
1040
1040-0.134
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: CNhs11228

Jaspar motifP-value
MA0002.20.00107
MA0003.10.157
MA0004.10.665
MA0006.10.125
MA0007.10.325
MA0009.10.582
MA0014.10.454
MA0017.11.89779e-6
MA0018.20.0647
MA0019.10.159
MA0024.10.631
MA0025.10.515
MA0027.10.0816
MA0028.10.526
MA0029.10.259
MA0030.10.986
MA0031.10.1
MA0035.20.0065
MA0038.10.0921
MA0039.20.0837
MA0040.10.55
MA0041.10.255
MA0042.10.59
MA0043.10.091
MA0046.12.86319e-14
MA0047.22.88853e-5
MA0048.10.4
MA0050.11.88117e-4
MA0051.10.0189
MA0052.11.37714e-4
MA0055.10.392
MA0057.10.134
MA0058.10.543
MA0059.10.354
MA0060.10.0071
MA0061.10.0659
MA0062.20.132
MA0065.21.32893e-6
MA0066.10.0732
MA0067.10.79
MA0068.10.767
MA0069.10.0353
MA0070.10.44
MA0071.10.0475
MA0072.10.0382
MA0073.10.689
MA0074.10.164
MA0076.10.951
MA0077.10.078
MA0078.10.601
MA0079.20.576
MA0080.23.5459e-10
MA0081.10.494
MA0083.16.77577e-4
MA0084.10.323
MA0087.10.73
MA0088.10.341
MA0090.10.0318
MA0091.10.255
MA0092.10.23
MA0093.10.688
MA0099.23.4404e-5
MA0100.10.989
MA0101.10.0993
MA0102.20.893
MA0103.10.0371
MA0104.20.767
MA0105.10.0178
MA0106.10.158
MA0107.10.0916
MA0108.27.16136e-4
MA0111.10.857
MA0112.25.68311e-5
MA0113.10.286
MA0114.13.13334e-5
MA0115.14.64768e-4
MA0116.10.0392
MA0117.10.894
MA0119.10.169
MA0122.10.972
MA0124.10.729
MA0125.10.13
MA0131.10.767
MA0135.10.435
MA0136.15.06838e-9
MA0137.20.139
MA0138.20.557
MA0139.10.221
MA0140.15.09718e-4
MA0141.11.98965e-4
MA0142.10.221
MA0143.10.114
MA0144.10.0624
MA0145.10.0542
MA0146.10.041
MA0147.10.876
MA0148.11.20069e-6
MA0149.10.0515
MA0150.10.0273
MA0152.10.261
MA0153.19.34583e-13
MA0154.10.017
MA0155.10.412
MA0156.14.80416e-5
MA0157.10.0346
MA0159.13.36566e-4
MA0160.10.00578
MA0162.10.267
MA0163.12.29065e-4
MA0164.10.926
MA0258.10.00188
MA0259.10.557



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: CNhs11228

Novel motifP-value
10.161
100.12
1000.727
1010.975
1020.852
1030.103
1040.957
1050.188
1060.0118
1070.0551
1080.853
1090.00533
110.0465
1100.0643
1110.0236
1120.0053
1130.776
1140.127
1150.591
1160.352
1170.0404
1180.438
1190.11
120.914
1200.665
1210.368
1220.899
1230.355
1240.356
1250.338
1260.0615
1270.0828
1280.0217
1290.0638
138.14349e-5
1300.754
1310.679
1320.937
1330.816
1340.379
1350.875
1360.104
1370.645
1380.847
1390.181
140.603
1400.0699
1410.151
1420.154
1430.283
1440.721
1450.0214
1460.414
1470.918
1480.508
1490.0618
150.147
1500.14
1510.413
1520.0596
1530.681
1540.957
1550.572
1560.0112
1570.454
1580.201
1590.96
1600.196
1610.0773
1620.996
1630.232
1640.0435
1650.0105
1660.782
1670.621
1680.275
1690.00595
170.0268
180.696
190.0749
20.667
200.463
210.49
220.108
230.323
240.035
250.566
263.53023e-4
270.738
280.447
290.0901
30.0505
300.807
310.706
320.289
330.222
340.621
350.915
360.484
370.0166
380.374
390.219
40.296
400.21
410.364
420.215
430.121
440.239
450.549
460.136
470.136
480.118
490.148
50.118
500.304
510.625
520.137
530.918
540.583
550.578
560.316
570.683
580.253
590.0329
60.974
600.0214
610.18
620.139
630.126
640.6
650.215
660.923
670.478
680.894
690.348
70.0321
700.0125
710.0174
720.433
730.0264
740.521
750.0936
760.942
770.197
780.00791
790.468
80.106
800.945
810.487
820.104
830.0778
840.854
850.0399
860.185
870.0626
880.209
890.292
90.383
900.161
910.177
920.141
930.0381
940.521
950.0478
960.203
970.976
980.522
990.244



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: CNhs11228


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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000349 (limbic system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0001954 (Ammon's horn)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002421 (hippocampal formation)
0002532 (epiblast (generic))
0002600 (limbic lobe)
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003022 (lobe parts of cerebral cortex)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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