Personal tools

FF:11643-122D5

From FANTOM5_SSTAR

Revision as of 20:13, 16 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:Mouse Neurons - dorsal spinal cord, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
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 numberRNADOR3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008726
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs12618

00
10.535
100
1000.0867
10000
1001-0.0668
10020.00807
10030.00203
10040
10050.0491
10060.605
1007-0.25
10080
1009-0.103
101-0.244
10100
10110.298
10120
10130.25
1014-6.860561e-4
10150.263
10160.12
10170
10180
10190
1020
10200.588
10210.0867
10220
10230
10240.0514
10250.06
10260.0572
10270.406
10280
1029-0.176
1030.0635
10300
1031-0.127
10320.408
10330
10340
10350
1036-0.179
10370
1038-0.0644
10390.0535
1040
1040-0.256
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: CNhs12618

Jaspar motifP-value
MA0002.20.00558
MA0003.10.583
MA0004.10.449
MA0006.10.228
MA0007.10.221
MA0009.10.893
MA0014.10.556
MA0017.12.34405e-6
MA0018.20.046
MA0019.10.972
MA0024.10.61
MA0025.10.757
MA0027.10.616
MA0028.10.0369
MA0029.10.916
MA0030.10.473
MA0031.10.0895
MA0035.20.0673
MA0038.10.405
MA0039.20.169
MA0040.10.54
MA0041.10.204
MA0042.10.535
MA0043.10.285
MA0046.14.18402e-7
MA0047.22.70993e-4
MA0048.10.0435
MA0050.11.47572e-6
MA0051.17.46617e-5
MA0052.10.475
MA0055.10.0295
MA0057.10.474
MA0058.10.517
MA0059.10.204
MA0060.10.0843
MA0061.10.0608
MA0062.22.36859e-4
MA0065.29.72105e-5
MA0066.10.0605
MA0067.10.891
MA0068.10.619
MA0069.10.0573
MA0070.10.239
MA0071.10.156
MA0072.10.127
MA0073.10.9
MA0074.10.235
MA0076.10.0936
MA0077.10.0655
MA0078.10.825
MA0079.20.117
MA0080.22.39885e-9
MA0081.10.29
MA0083.10.14
MA0084.10.268
MA0087.10.306
MA0088.10.178
MA0090.10.0913
MA0091.10.303
MA0092.10.254
MA0093.10.494
MA0099.20.00463
MA0100.10.0823
MA0101.10.0321
MA0102.20.48
MA0103.10.152
MA0104.20.925
MA0105.10.0216
MA0106.10.0526
MA0107.10.0538
MA0108.20.672
MA0111.10.997
MA0112.24.12756e-4
MA0113.10.231
MA0114.11.13147e-5
MA0115.11.29803e-4
MA0116.10.102
MA0117.10.467
MA0119.10.197
MA0122.10.849
MA0124.10.562
MA0125.10.172
MA0131.10.555
MA0135.10.0302
MA0136.14.85043e-11
MA0137.20.00728
MA0138.20.0107
MA0139.10.552
MA0140.12.16179e-4
MA0141.10.0598
MA0142.10.792
MA0143.10.796
MA0144.10.0209
MA0145.10.114
MA0146.10.0459
MA0147.10.79
MA0148.14.88007e-5
MA0149.10.145
MA0150.10.016
MA0152.10.0304
MA0153.19.59236e-7
MA0154.10.0389
MA0155.10.92
MA0156.12.07301e-8
MA0157.10.0679
MA0159.10.00238
MA0160.10.0385
MA0162.10.315
MA0163.10.00238
MA0164.10.885
MA0258.10.021
MA0259.10.824



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: CNhs12618

Novel motifP-value
10.114
100.0371
1000.489
1010.751
1020.873
1030.0766
1040.601
1050.64
1060.0757
1070.156
1080.319
1090.0159
110.105
1100.0277
1110.0414
1120.00146
1130.764
1140.147
1150.981
1160.949
1170.00221
1180.219
1190.141
120.936
1200.677
1210.179
1220.773
1230.00923
1240.131
1250.389
1260.0545
1270.121
1280.0772
1290.329
131.34149e-6
1300.355
1310.817
1320.584
1330.737
1340.278
1350.154
1360.429
1370.34
1380.894
1390.266
140.968
1400.0385
1410.391
1420.046
1430.528
1440.977
1450.00106
1460.589
1470.558
1480.627
1490.942
150.0989
1500.0831
1510.705
1520.163
1530.309
1540.488
1550.993
1560.00501
1570.154
1580.0273
1590.0568
1600.244
1610.223
1620.728
1630.431
1640.00537
1650.303
1660.743
1670.61
1680.706
1690.00222
170.0729
180.968
190.14
20.441
200.0305
210.488
220.214
230.587
240.13
250.727
264.35304e-8
270.378
280.497
290.0242
30.0586
300.606
310.754
320.969
330.14
340.683
350.874
360.439
370.0267
380.484
390.438
40.49
400.593
410.568
420.144
430.12
440.937
450.87
460.0289
470.305
480.188
490.104
50.0848
500.394
510.738
520.646
530.641
540.924
550.93
560.578
570.501
580.27
590.316
60.86
600.0547
610.0584
620.149
630.211
640.808
650.398
660.822
670.784
680.69
690.849
70.014
700.0583
710.00537
720.619
730.0348
740.33
750.038
760.278
770.638
780.00736
790.566
80.0771
800.715
810.736
820.306
830.51
840.82
850.183
860.107
870.764
880.142
890.508
90.53
900.0478
910.253
920.413
930.0333
940.326
950.0882
960.167
970.96
980.695
990.778



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: CNhs12618


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)
0002611 (neuron of the dorsal 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)
0002256 (dorsal 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)
0000206 (mouse neuron of the dorsal 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)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11643-122D5&oldid=3076960"