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|profile_rnaseq=,,,
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|repeat_enrich_byfamily=0.0452080467040714,0,0,0,0,0,-0.133380731197635,0,0,0,0,0.0532676794741855,0,0,0,0,0,0,0.0941131483315104,0,0,0,0,0,0,0,0,0,0,0,0,0.379520168325414,-0.484191857165363,0,0,0,0,0.0462159258322438,-0.140519265560463,0.229222520918703,-0.0346174416872684,0.359455902695425,0.815920067114044,0.192901363035279,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,-0.081470329825696,-0.310650657339386,0.0838531389718853,-0.0593831718178933,0,-0.0780086007519514,0.168985880002793,0.192901363035279,0,0,0.11904012428753,0.183977858107347,0.170972574605164,-0.0788315948399074,0,0,0,0,0,0,0.125014287660718,-0.0206293412310332,-0.0523802298422757,0,0,0.0742309351586685,0.323199110136342,0
|rna_box=122
|rna_box=122
|rna_catalog_number=custom
|rna_catalog_number=custom

Revision as of 10:27, 24 September 2012


Name:Mouse Neurons - ventral spinal cord, donor3
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 numberRNAMSC1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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

CNhs12113

00
10.457
100
1000.286
10000
1001-0.0668
10020.0198
10030.0753
10040.0371
1005-0.0257
10060.422
1007-0.0517
10080
1009-0.2
101-0.0956
10100
10110.26
10120
1013-0.0423
10140.0508
10150.3
10160.253
10170
10180
10190
1020
10200.463
10210.0742
1022-0.0498
10230
1024-0.14
10250
10260
10270.278
10280
1029-0.0452
103-0.0405
10300
1031-0.224
1032-0.0389
1033-0.0665
10340
10350.0742
1036-0.139
10370
10380.106
1039-0.179
1040
1040-0.245
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: CNhs12113

Jaspar motifP-value
MA0002.22.66653e-4
MA0003.10.189
MA0004.10.703
MA0006.10.144
MA0007.10.13
MA0009.10.919
MA0014.10.55
MA0017.11.68141e-5
MA0018.20.0213
MA0019.10.558
MA0024.10.688
MA0025.10.472
MA0027.10.801
MA0028.10.37
MA0029.10.799
MA0030.10.428
MA0031.10.0431
MA0035.20.0397
MA0038.10.23
MA0039.20.0618
MA0040.10.588
MA0041.10.173
MA0042.10.465
MA0043.10.146
MA0046.11.37939e-8
MA0047.25.44481e-5
MA0048.10.316
MA0050.12.81428e-7
MA0051.11.86522e-4
MA0052.10.0522
MA0055.10.328
MA0057.10.169
MA0058.10.754
MA0059.10.338
MA0060.10.00464
MA0061.10.0555
MA0062.20.0726
MA0065.21.01454e-5
MA0066.10.0518
MA0067.10.571
MA0068.10.459
MA0069.10.0477
MA0070.10.0462
MA0071.10.123
MA0072.10.09
MA0073.10.967
MA0074.10.364
MA0076.10.855
MA0077.10.0437
MA0078.10.431
MA0079.20.411
MA0080.21.36865e-10
MA0081.10.483
MA0083.10.0584
MA0084.10.513
MA0087.10.473
MA0088.10.189
MA0090.10.0607
MA0091.10.154
MA0092.10.158
MA0093.10.756
MA0099.21.82694e-4
MA0100.10.551
MA0101.10.0648
MA0102.20.926
MA0103.10.0984
MA0104.20.849
MA0105.10.0221
MA0106.10.072
MA0107.10.0563
MA0108.20.198
MA0111.10.9
MA0112.26.51549e-5
MA0113.10.156
MA0114.17.49936e-5
MA0115.10.00195
MA0116.10.0544
MA0117.10.749
MA0119.10.0934
MA0122.10.728
MA0124.10.951
MA0125.10.178
MA0131.10.832
MA0135.10.182
MA0136.12.352e-9
MA0137.20.141
MA0138.20.123
MA0139.10.271
MA0140.10.00236
MA0141.10.00693
MA0142.10.121
MA0143.10.203
MA0144.10.0498
MA0145.10.0516
MA0146.10.0239
MA0147.10.992
MA0148.17.62196e-6
MA0149.10.0915
MA0150.10.0402
MA0152.10.0749
MA0153.15.15142e-8
MA0154.10.0155
MA0155.10.51
MA0156.11.47699e-5
MA0157.10.0246
MA0159.10.00412
MA0160.10.0458
MA0162.10.264
MA0163.10.00138
MA0164.10.995
MA0258.10.00462
MA0259.10.779



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: CNhs12113

Novel motifP-value
10.124
100.0723
1000.755
1010.836
1020.806
1030.0956
1040.747
1050.249
1060.0157
1070.0835
1080.483
1090.00561
110.0695
1100.0722
1110.0562
1120.0038
1130.898
1140.206
1150.606
1160.493
1170.0229
1180.276
1190.0891
120.829
1200.727
1210.336
1220.697
1230.156
1240.653
1250.456
1260.233
1270.1
1280.0388
1290.134
134.26538e-5
1300.321
1310.506
1320.971
1330.672
1340.402
1350.935
1360.168
1370.499
1380.992
1390.132
140.576
1400.0838
1410.208
1420.142
1430.367
1440.935
1450.0107
1460.418
1470.781
1480.447
1490.195
150.0866
1500.141
1510.413
1520.0803
1530.541
1540.771
1550.729
1569.41785e-4
1570.279
1580.0926
1590.0562
1600.204
1610.228
1620.782
1630.302
1640.0257
1650.0276
1660.745
1670.903
1680.587
1690.00225
170.024
180.976
190.0709
20.842
200.292
210.408
220.0945
230.25
240.0312
250.658
263.31154e-5
270.884
280.451
290.0898
30.0667
300.839
310.909
320.475
330.206
340.646
350.945
360.354
370.0196
380.318
390.229
40.569
400.302
410.553
420.163
430.117
440.639
450.581
460.0654
470.185
480.096
490.126
50.0977
500.321
510.6
520.22
530.809
540.707
550.862
560.337
570.543
580.219
590.0762
60.722
600.0211
610.115
620.0924
630.108
640.723
650.194
660.931
670.577
680.484
690.477
70.0256
700.0095
710.0131
720.383
730.0289
740.251
750.0775
760.616
770.257
780.0311
790.942
80.0809
800.809
810.672
820.208
830.282
840.749
850.0556
860.238
870.313
880.225
890.225
90.335
900.0759
910.293
920.357
930.0232
940.7
950.0519
960.321
970.87
980.595
990.335



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: CNhs12113


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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