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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11812
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11812
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11812
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11812
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep3.CNhs13089.11812-124E3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep3.CNhs13089.11812-124E3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep3.CNhs13089.11812-124E3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep3.CNhs13089.11812-124E3.mm10.nobarcode.ctss.bed.gz

Revision as of 17:09, 4 August 2017


Name:neurospheres - enteric neuron derived, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs13089
Sample type:primary cells
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 numberEN3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005099
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13089 CAGE DRX008864 DRR009736
Accession ID Mm9

Library idBAMCTSS
CNhs13089 DRZ001161 DRZ002546
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs13089

00
10.0847
100
1000.0847
1000-0.0355
10010.0179
1002-0.102
1003-0.0162
10040
1005-0.0389
10060.127
1007-0.0212
10080
1009-0.0572
101-0.0382
10100
1011-0.0279
10120
1013-0.0497
1014-0.00982
10150.132
10160.382
10170
10180
10190
1020
10200.528
10210.201
1022-0.315
10230
10240
1025-0.0611
10260
10270.468
10280
1029-0.0213
103-0.0719
10300
10310.359
10320.0414
10330.141
10340
10350
10360.0291
10370
1038-0.00837
1039-0.241
1040
10400.243
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



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: CNhs13089

Jaspar motifP-value
MA0002.21.42633e-5
MA0003.10.0215
MA0004.10.903
MA0006.10.371
MA0007.10.469
MA0009.10.108
MA0014.10.677
MA0017.13.81433e-6
MA0018.20.00639
MA0019.10.435
MA0024.10.0022
MA0025.10.629
MA0027.10.19
MA0028.10.799
MA0029.10.178
MA0030.10.548
MA0031.10.103
MA0035.28.35721e-4
MA0038.10.0561
MA0039.20.086
MA0040.10.776
MA0041.10.487
MA0042.10.778
MA0043.10.123
MA0046.11.64183e-13
MA0047.24.55204e-4
MA0048.10.495
MA0050.10.00453
MA0051.10.0524
MA0052.16.52843e-5
MA0055.10.545
MA0057.10.0923
MA0058.10.843
MA0059.10.351
MA0060.13.58721e-6
MA0061.10.0304
MA0062.20.524
MA0065.23.09663e-6
MA0066.10.131
MA0067.10.709
MA0068.10.334
MA0069.10.513
MA0070.10.0356
MA0071.10.131
MA0072.10.508
MA0073.10.919
MA0074.10.554
MA0076.10.551
MA0077.10.0497
MA0078.10.383
MA0079.20.675
MA0080.26.66875e-11
MA0081.10.465
MA0083.10.699
MA0084.10.429
MA0087.10.834
MA0088.10.917
MA0090.10.518
MA0091.10.627
MA0092.10.827
MA0093.10.954
MA0099.20.0166
MA0100.10.524
MA0101.10.157
MA0102.20.676
MA0103.10.0017
MA0104.20.849
MA0105.15.77945e-4
MA0106.10.949
MA0107.10.0616
MA0108.20.00251
MA0111.10.877
MA0112.25.08362e-6
MA0113.10.165
MA0114.13.29012e-5
MA0115.10.0148
MA0116.10.00161
MA0117.10.647
MA0119.10.093
MA0122.10.75
MA0124.10.848
MA0125.10.115
MA0131.10.53
MA0135.10.038
MA0136.13.46439e-8
MA0137.20.468
MA0138.20.465
MA0139.10.126
MA0140.16.02301e-5
MA0141.10.00276
MA0142.10.058
MA0143.10.398
MA0144.10.248
MA0145.10.0402
MA0146.10.527
MA0147.10.677
MA0148.10.00427
MA0149.10.962
MA0150.10.0595
MA0152.10.461
MA0153.11.84587e-13
MA0154.10.00356
MA0155.10.512
MA0156.11.59173e-4
MA0157.10.044
MA0159.10.0644
MA0160.10.0221
MA0162.10.185
MA0163.10.00383
MA0164.10.691
MA0258.10.00605
MA0259.10.955



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: CNhs13089

Novel motifP-value
10.145
100.0923
1000.961
1010.72
1020.987
1030.128
1040.577
1050.045
1060.0235
1070.105
1080.929
1090.0419
110.121
1100.13
1110.00912
1120.0262
1130.553
1140.0384
1150.791
1160.445
1170.249
1180.357
1190.032
120.485
1200.293
1210.281
1220.367
1230.843
1240.281
1250.835
1260.471
1270.142
1280.0645
1290.153
130.0137
1300.658
1310.397
1320.434
1330.9
1340.661
1350.633
1360.86
1370.381
1380.966
1390.0593
140.553
1400.0149
1410.196
1420.747
1430.472
1440.973
1450.21
1460.418
1470.867
1480.46
1490.132
150.108
1500.338
1510.321
1520.0813
1530.873
1540.87
1550.685
1567.07185e-14
1570.31
1580.608
1590.405
1600.148
1610.113
1620.899
1630.896
1640.109
1650.0682
1660.639
1670.36
1680.526
1690.0123
170.0493
180.786
190.171
20.57
200.7
210.324
220.272
230.214
240.0953
250.395
260.0243
270.386
280.424
290.447
30.0738
300.666
310.782
320.102
330.471
340.295
350.901
360.552
370.0627
380.204
390.237
40.576
400.325
410.44
420.283
430.186
440.212
450.302
460.158
470.232
480.153
490.151
50.25
500.422
510.508
520.331
530.436
540.472
550.688
560.548
570.603
580.128
590.0337
60.615
600.0869
610.283
620.0602
630.0664
640.472
650.105
660.69
670.879
680.39
690.85
70.0561
700.00179
710.0737
720.304
730.115
740.848
750.134
760.623
770.14
780.0337
790.329
80.126
800.684
810.691
820.0522
830.102
840.961
850.139
860.232
870.719
880.671
890.025
90.414
900.51
910.342
920.211
930.578
940.518
950.111
960.554
970.727
980.189
990.268



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: CNhs13089


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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0002005 (enteric nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011142 (mouse neurospheres - enteric neuron derived sample)

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
CL:0000133 (neurectodermal cell)
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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