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FF:11725-123D6

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Name:Mouse Neurons - ventral spinal cord, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNASPI1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs12632

00
10.599
100
1000.112
10000
1001-0.0275
10020.175
10030.14
10040
10050
10060.503
1007-0.215
10080
1009-0.148
101-0.145
10100
10110.259
10120.112
10130
10140.112
10150.133
10160.288
10170
10180
10190
1020
10200.563
10210
10220
10230
10240
10250.112
10260.0763
10270.507
10280
1029-0.018
1030.0545
10300
1031-0.139
10320.299
1033-0.0418
10340
10350.112
1036-0.189
10370
10380.063
1039-0.0102
1040
1040-0.216
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: CNhs12632

Jaspar motifP-value
MA0002.28.35172e-4
MA0003.10.294
MA0004.10.426
MA0006.10.184
MA0007.10.227
MA0009.10.698
MA0014.10.49
MA0017.17.47927e-7
MA0018.20.149
MA0019.10.447
MA0024.10.968
MA0025.10.787
MA0027.10.263
MA0028.10.0232
MA0029.10.896
MA0030.10.212
MA0031.10.0083
MA0035.20.00405
MA0038.10.479
MA0039.20.0226
MA0040.10.357
MA0041.10.272
MA0042.10.481
MA0043.10.766
MA0046.12.50377e-11
MA0047.22.00594e-6
MA0048.10.128
MA0050.11.89313e-6
MA0051.18.13548e-5
MA0052.10.0292
MA0055.10.0318
MA0057.10.277
MA0058.10.355
MA0059.10.228
MA0060.10.384
MA0061.10.0814
MA0062.24.01976e-5
MA0065.24.0135e-6
MA0066.10.0686
MA0067.10.954
MA0068.10.708
MA0069.10.0584
MA0070.10.633
MA0071.10.104
MA0072.10.0849
MA0073.10.966
MA0074.10.129
MA0076.10.0456
MA0077.10.169
MA0078.10.857
MA0079.20.384
MA0080.24.19789e-10
MA0081.10.18
MA0083.10.0654
MA0084.10.722
MA0087.10.345
MA0088.10.13
MA0090.10.0749
MA0091.10.235
MA0092.10.197
MA0093.10.44
MA0099.21.99782e-4
MA0100.10.263
MA0101.10.0354
MA0102.20.735
MA0103.10.101
MA0104.20.84
MA0105.10.0629
MA0106.10.109
MA0107.10.0771
MA0108.20.0255
MA0111.10.938
MA0112.21.85186e-4
MA0113.10.106
MA0114.11.39515e-5
MA0115.11.8405e-4
MA0116.10.0676
MA0117.10.685
MA0119.10.158
MA0122.10.709
MA0124.10.959
MA0125.10.213
MA0131.10.796
MA0135.10.922
MA0136.12.063e-13
MA0137.20.143
MA0138.20.0235
MA0139.10.4
MA0140.12.45483e-4
MA0141.10.00765
MA0142.10.156
MA0143.10.621
MA0144.10.0975
MA0145.10.0589
MA0146.10.0143
MA0147.10.693
MA0148.11.21883e-6
MA0149.10.109
MA0150.10.0178
MA0152.10.0459
MA0153.11.32653e-11
MA0154.10.0369
MA0155.10.615
MA0156.14.40462e-10
MA0157.10.0197
MA0159.10.00388
MA0160.10.027
MA0162.10.281
MA0163.10.00147
MA0164.10.938
MA0258.10.0074
MA0259.10.942



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: CNhs12632

Novel motifP-value
10.14
100.0828
1000.544
1010.684
1020.784
1030.116
1040.75
1050.258
1060.0547
1070.17
1080.391
1090.00537
110.0644
1100.0383
1110.0487
1120.00338
1130.768
1140.158
1150.815
1160.69
1170.00484
1180.283
1190.1
120.856
1200.674
1210.0531
1220.524
1230.00692
1240.19
1250.553
1260.054
1270.131
1280.051
1290.0969
132.17071e-6
1300.147
1310.374
1320.702
1330.762
1340.217
1350.287
1360.125
1370.935
1380.986
1390.218
140.755
1400.211
1410.358
1420.278
1430.544
1440.759
1450.00296
1460.261
1470.439
1480.795
1490.474
150.103
1500.115
1510.478
1520.0871
1530.713
1540.681
1550.518
1564.09073e-4
1570.245
1580.044
1590.422
1600.288
1610.146
1620.684
1630.376
1640.0159
1650.0656
1660.966
1670.81
1680.444
1690.00171
170.0307
180.992
190.112
20.805
200.0805
210.271
220.111
230.6
240.0239
250.653
262.52317e-6
270.617
280.499
290.058
30.0551
300.981
310.806
320.988
330.124
340.795
350.984
360.305
370.0177
380.42
390.417
40.534
400.205
410.276
420.158
430.129
440.874
450.619
460.0596
470.199
480.13
490.145
50.112
500.31
510.617
520.365
530.928
540.732
550.819
560.468
570.678
580.251
590.107
60.896
600.038
610.0731
620.11
630.115
640.63
650.278
660.772
670.703
680.543
690.461
70.0204
700.0157
710.0105
720.383
730.0233
740.667
750.0433
760.513
770.354
780.00911
790.231
80.0856
800.595
810.8
820.194
830.103
840.947
850.12
860.162
870.102
880.247
890.236
90.414
900.135
910.448
920.423
930.0314
940.858
950.0244
960.174
970.819
980.441
990.663



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: CNhs12632


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)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002612 (neuron of the ventral spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002257 (ventral horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000207 (mouse neuron of the ventral spinal cord 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:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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