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{{f5samples
{{f5samples
|id=FF:11808-124D8
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000011,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|name=neurospheres - parasympathetic neuron derived, biol_rep2
|sample_id=11808
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|rna_position=D8
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|sample_cell_catalog=
|sample_company=
|rna_lot_number=para2
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=
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|sample_tissue=ANATOMICAL SYSTEM
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|sample_sex=
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|sample_cell_type=
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|sample_collaboration=Hideki Enomoto (RIKEN CDB)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=12
|rna_concentration=0.52
|sample_note=
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|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000031,CL:0000034,CL:0000047,CL:0000048,CL:0000055,CL:0000107,CL:0000133,CL:0000144,CL:0000211,CL:0000220,CL:0000221,CL:0000255,CL:0000393,CL:0000404,CL:0000540,CL:0000548,CL:0000723,CL:0002319,CL:0002321,CL:0002371
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|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000011,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|ancestors_in_disease_facet=
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|sample_description=
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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:11808-124D8
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011143
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011143
|name=neurospheres - parasympathetic neuron derived, biol_rep2
|namespace=
|namespace=
|part_of=UBERON:0000011
|part_of=UBERON:0000011
|profile_cagescan=,,,
|profile_hcage=CNhs13085,LSID1000,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=124
|rna_catalog_number=
|rna_concentration=0.52
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=para2
|rna_od260/230=
|rna_od260/280=
|rna_position=D8
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=124D8
|rna_weight_ug=12
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=
|sample_collaboration=Hideki Enomoto (RIKEN CDB)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11808
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=ANATOMICAL SYSTEM
|top_motifs=SOX2:1.94861870455;SOX5:1.8834408657;RXR{A,B,G}:1.57888067216;EN1,2:1.50862319895;ONECUT1,2:1.49632849425;TP53:1.48278086486;SREBF1,2:1.45062829577;GZF1:1.32868598177;ZNF143:1.3071023975;ZNF384:1.24037851087;SOX17:1.22683956453;NKX2-1,4:1.11883782546;CDC5L:1.08161434332;JUN:1.0692222552;AHR_ARNT_ARNT2:1.04071242041;NRF1:1.01046577309;POU3F1..4:0.996938159159;NANOG:0.991622838768;PRRX1,2:0.963366795001;ZFP161:0.927077716951;ATF4:0.882746691023;FOXD3:0.835119920543;HMX1:0.834063899066;FOSL2:0.81854076182;GFI1:0.796050840208;DBP:0.759860294529;TFDP1:0.71008719143;MTE{core}:0.709870890223;SOX{8,9,10}:0.675318861124;MZF1:0.660146707151;TFAP2{A,C}:0.644511664855;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.644326370309;ELK1,4_GABP{A,B1}:0.634003901535;RORA:0.627592624861;EVI1:0.605694017339;LHX3,4:0.604249601787;FOXQ1:0.587566523964;HBP1_HMGB_SSRP1_UBTF:0.581039701085;PBX1:0.570556541796;AIRE:0.561441535045;LEF1_TCF7_TCF7L1,2:0.546164604375;PDX1:0.544928788839;MED-1{core}:0.543660977772;ZBTB16:0.538728726973;TFAP2B:0.512488917252;PAX8:0.512438014516;EGR1..3:0.511653810736;NHLH1,2:0.508329104225;IKZF1:0.503685104695;NFE2:0.503081091434;RFX2..5_RFXANK_RFXAP:0.50262246647;NKX3-1:0.501030138585;GATA4:0.496778706941;PATZ1:0.472789746613;ADNP_IRX_SIX_ZHX:0.45276322013;FOS_FOS{B,L1}_JUN{B,D}:0.446750486969;PAX5:0.44021332062;MAZ:0.425692174866;EP300:0.411736837845;SP1:0.391602344703;GTF2I:0.385915359277;HAND1,2:0.383452265836;VSX1,2:0.341950944559;ATF2:0.315840232552;NFY{A,B,C}:0.305799251242;ZNF148:0.300394991719;BREu{core}:0.299829239866;GTF2A1,2:0.293280631528;RBPJ:0.284120969208;CREB1:0.281831647367;TFAP4:0.278706125839;UFEwm:0.27515434975;TFCP2:0.273836928328;ZBTB6:0.26948603672;TEF:0.268986282981;BACH2:0.246170836072;E2F1..5:0.2236842021;HIC1:0.218253360134;IKZF2:0.210288237206;NR1H4:0.204766606529;PAX4:0.188019030811;OCT4_SOX2{dimer}:0.18015137096;EBF1:0.169253544273;TEAD1:0.151923153482;STAT1,3:0.149381216081;MYFfamily:0.142383452096;RFX1:0.14147561017;REST:0.140798301165;POU5F1:0.139638514821;ATF5_CREB3:0.131622739364;HES1:0.129502591948;CRX:0.125825502929;XCPE1{core}:0.121106304946;RREB1:0.109377534098;FOXP3:0.109112056923;HIF1A:0.10907924138;FOX{I1,J2}:0.0852726042196;NFE2L1:0.0627595469044;HMGA1,2:0.0528303231532;FOX{D1,D2}:0.0400796832841;NKX3-2:0.0243442843057;HSF1,2:0.0217834952106;PRDM1:0.00511996786593;ZNF238:-0.00472675640108;POU2F1..3:-0.0054427461347;MYB:-0.00600275026113;GFI1B:-0.00778703005267;SMAD1..7,9:-0.0233469074432;FOXO1,3,4:-0.0242365334244;HOX{A4,D4}:-0.0392263013844;ZNF423:-0.0458855824166;STAT5{A,B}:-0.0588092912837;KLF4:-0.0590372588381;FOXP1:-0.063566703052;ZIC1..3:-0.0743816289596;ATF6:-0.0901527946441;ESR1:-0.113619358712;TLX2:-0.129910814625;CUX2:-0.13475062451;DMAP1_NCOR{1,2}_SMARC:-0.140795951761;SPZ1:-0.141526468097;TLX1..3_NFIC{dimer}:-0.152054183008;ALX1:-0.160460476939;ESRRA:-0.165767346062;PAX1,9:-0.179085523227;MTF1:-0.186871096106;SPIB:-0.1951463749;YY1:-0.213822217625;PITX1..3:-0.216956354792;NKX2-2,8:-0.24275793477;MYBL2:-0.244255224354;NFIL3:-0.244416450536;NFATC1..3:-0.262077103987;FOXM1:-0.26934779535;RUNX1..3:-0.283517958878;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.291368830144;GCM1,2:-0.296222519538;FOXL1:-0.30926221525;HOXA9_MEIS1:-0.32029774867;BPTF:-0.345979545643;CEBPA,B_DDIT3:-0.376304909926;AR:-0.380315622669;IRF1,2:-0.387626670847;IRF7:-0.391890418752;ELF1,2,4:-0.401909209897;TOPORS:-0.407600310183;T:-0.410364258354;STAT2,4,6:-0.420302671891;POU1F1:-0.423827692659;TAL1_TCF{3,4,12}:-0.425387595078;HNF4A_NR2F1,2:-0.457838408033;PAX6:-0.464594763695;NR6A1:-0.487070440782;MEF2{A,B,C,D}:-0.490580291066;SPI1:-0.512095010703;bHLH_family:-0.555718431032;NFKB1_REL_RELA:-0.564369489139;HNF1A:-0.597220028122;LMO2:-0.604746853462;SRF:-0.605843119449;FOX{F1,F2,J1}:-0.609667374161;NKX6-1,2:-0.612455210182;NFIX:-0.613833319348;NR3C1:-0.642521114549;POU6F1:-0.64629613732;ALX4:-0.647344611921;FOXA2:-0.661056180289;ARID5B:-0.665785325281;CDX1,2,4:-0.679580327285;GLI1..3:-0.690663337996;NANOG{mouse}:-0.697539187604;NFE2L2:-0.725387981963;ETS1,2:-0.739821022559;MYOD1:-0.744006980047;HLF:-0.783532878859;TGIF1:-0.784331061327;TBP:-0.808154783463;PAX2:-0.820938165252;NKX2-3_NKX2-5:-0.823342273315;RXRA_VDR{dimer}:-0.824034158075;MAFB:-0.890140407264;NR5A1,2:-0.938580196604;GATA6:-0.991910316281;FOXN1:-1.03413893935;HOX{A5,B5}:-1.1381775571;PPARG:-1.15518599222;SNAI1..3:-1.23771791527;ZEB1:-1.5568442938;TBX4,5:-2.11423826572
}}
}}

Revision as of 15:02, 21 March 2012


Name:neurospheres - parasympathetic neuron derived, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberpara2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13085

00
10.00311
100
1000
1000-0.0279
10010.00433
1002-0.101
1003-0.0687
10040
1005-0.0666
1006-0.074
10070.0353
10080
1009-0.0399
1010.0119
10100
1011-0.012
10120
1013-0.118
10140
10150.205
10160.456
10170
10180
10190
1020
10200.277
10210.16
1022-0.177
10230
10240
1025-0.0611
10260
10270.444
10280
1029-0.0228
103-0.0787
10300
10310.385
10320.117
10330.0874
10340
10350
1036-0.0061
10370
10380.0344
1039-0.29
1040
10400.159
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: CNhs13085

Jaspar motifP-value
MA0002.20.00206
MA0003.10.00358
MA0004.10.854
MA0006.10.275
MA0007.10.816
MA0009.10.0397
MA0014.10.805
MA0017.13.58791e-5
MA0018.29.13955e-4
MA0019.10.878
MA0024.10.0254
MA0025.10.504
MA0027.10.664
MA0028.10.24
MA0029.10.286
MA0030.10.915
MA0031.10.185
MA0035.22.70397e-4
MA0038.10.375
MA0039.20.268
MA0040.10.662
MA0041.10.0545
MA0042.10.798
MA0043.10.0398
MA0046.11.11785e-17
MA0047.20.00352
MA0048.10.742
MA0050.10.00303
MA0051.10.00394
MA0052.10.00294
MA0055.10.842
MA0057.10.154
MA0058.10.527
MA0059.10.357
MA0060.10.0011
MA0061.10.0448
MA0062.20.46
MA0065.24.18308e-5
MA0066.10.596
MA0067.10.272
MA0068.10.533
MA0069.10.401
MA0070.10.0195
MA0071.10.156
MA0072.10.459
MA0073.10.988
MA0074.10.642
MA0076.10.124
MA0077.10.0307
MA0078.10.157
MA0079.20.295
MA0080.24.9489e-8
MA0081.10.737
MA0083.10.0994
MA0084.10.92
MA0087.10.53
MA0088.10.661
MA0090.10.994
MA0091.10.841
MA0092.10.72
MA0093.10.745
MA0099.20.347
MA0100.10.472
MA0101.10.26
MA0102.20.874
MA0103.12.26963e-4
MA0104.20.963
MA0105.14.96889e-5
MA0106.10.13
MA0107.10.0952
MA0108.20.0129
MA0111.10.8
MA0112.29.57361e-5
MA0113.10.286
MA0114.17.00781e-5
MA0115.10.143
MA0116.19.73195e-4
MA0117.10.739
MA0119.10.0971
MA0122.10.9
MA0124.10.664
MA0125.10.181
MA0131.10.337
MA0135.10.556
MA0136.14.24004e-5
MA0137.20.465
MA0138.20.0115
MA0139.10.021
MA0140.13.79431e-4
MA0141.10.00653
MA0142.10.0966
MA0143.10.123
MA0144.10.697
MA0145.10.11
MA0146.10.669
MA0147.10.786
MA0148.10.00448
MA0149.10.417
MA0150.10.187
MA0152.10.915
MA0153.12.60193e-11
MA0154.10.00487
MA0155.10.668
MA0156.10.00559
MA0157.10.0253
MA0159.10.363
MA0160.10.0689
MA0162.10.185
MA0163.10.0131
MA0164.10.5
MA0258.10.023
MA0259.10.723



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: CNhs13085

Novel motifP-value
10.158
100.151
1000.715
1010.785
1020.746
1030.0886
1040.986
1050.104
1060.0183
1070.0904
1080.79
1090.0748
110.0918
1100.302
1110.019
1120.0488
1130.377
1140.0423
1150.378
1160.545
1170.528
1180.57
1190.0508
120.512
1200.44
1210.0841
1220.603
1230.829
1240.732
1250.704
1260.309
1270.427
1280.0247
1290.0796
130.1
1300.609
1310.425
1320.374
1330.281
1340.736
1350.316
1360.752
1370.372
1380.376
1390.163
140.402
1400.0315
1410.168
1420.52
1430.903
1440.54
1450.391
1460.544
1470.884
1480.707
1490.152
150.0991
1500.617
1510.334
1520.0941
1530.69
1540.682
1550.787
1561.43764e-4
1570.275
1580.811
1590.329
1600.112
1610.78
1620.925
1630.311
1640.137
1650.134
1660.759
1670.567
1680.96
1690.00958
170.0597
180.644
190.111
20.429
200.988
210.365
220.447
230.313
240.435
250.323
260.0563
270.234
280.591
290.676
30.119
300.59
310.757
320.105
330.371
340.365
350.534
360.614
370.146
380.27
390.353
40.738
400.415
410.739
420.296
430.249
440.349
450.391
460.219
470.164
480.2
490.182
50.233
500.831
510.49
520.224
530.342
540.555
550.568
560.618
570.417
580.0723
590.0282
60.998
600.0858
610.435
620.032
630.211
640.477
650.178
660.52
670.718
680.629
690.808
70.102
700.0304
710.147
720.462
730.212
740.222
750.236
760.839
770.258
780.0883
790.277
80.103
800.387
810.614
820.0306
830.161
840.506
850.0794
860.341
870.587
880.498
890.0603
90.375
900.73
910.227
920.0696
930.494
940.194
950.249
960.277
970.802
980.0835
990.109



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: CNhs13085


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000107 (autonomic neuron)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000010 (peripheral nervous system)
0000011 (parasympathetic nervous system)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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