Personal tools

FF:11722-123D3

From FANTOM5_SSTAR

Jump to: navigation, search


Name:Mouse Neurons - raphe, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12631
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueraphe nuclei
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 numberRNARAP2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005499
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12631 CAGE DRX008840 DRR009712
Accession ID Mm9

Library idBAMCTSS
CNhs12631 DRZ001137 DRZ002522
Accession ID Mm10

Library idBAMCTSS
CNhs12631 DRZ012487 DRZ013872
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

CNhs12631

00
10.733
100
1000
10000
10010
1002-0.0941
1003-0.0029
10040
10050
10060.693
1007-0.198
10080
1009-0.2
101-0.246
10100
10110.19
10120
10130.407
1014-0.0851
1015-0.212
10160.0537
10170
10180
10190
1020
10200.322
1021-0.0487
1022-0.0704
10230
1024-0.0899
10250
10260
10270.416
10280
1029-0.148
103-0.0848
10300
1031-0.46
10320.638
10330.247
10340
10350
1036-0.328
10370
1038-0.194
10393.171674e-4
1040
1040-0.268
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: CNhs12631

Jaspar motifP-value
MA0002.20.074
MA0003.10.371
MA0004.10.455
MA0006.10.166
MA0007.10.339
MA0009.10.771
MA0014.10.727
MA0017.12.18456e-5
MA0018.20.0071
MA0019.10.406
MA0024.10.00277
MA0025.10.00113
MA0027.10.129
MA0028.10.00447
MA0029.10.851
MA0030.10.977
MA0031.10.223
MA0035.20.0723
MA0038.10.569
MA0039.20.00433
MA0040.10.741
MA0041.10.188
MA0042.10.395
MA0043.10.0848
MA0046.13.37696e-6
MA0047.20.00303
MA0048.10.0136
MA0050.11.7241e-8
MA0051.11.99282e-6
MA0052.10.525
MA0055.14.46814e-4
MA0057.10.388
MA0058.10.471
MA0059.10.324
MA0060.10.0853
MA0061.10.0276
MA0062.22.18002e-6
MA0065.23.99705e-5
MA0066.10.162
MA0067.10.653
MA0068.10.288
MA0069.10.11
MA0070.10.179
MA0071.10.437
MA0072.10.618
MA0073.10.553
MA0074.10.278
MA0076.10.00989
MA0077.10.118
MA0078.10.429
MA0079.20.631
MA0080.21.10516e-9
MA0081.10.171
MA0083.17.51594e-4
MA0084.10.351
MA0087.10.0793
MA0088.10.312
MA0090.10.177
MA0091.10.465
MA0092.10.0956
MA0093.10.482
MA0099.20.0109
MA0100.10.216
MA0101.10.00431
MA0102.20.5
MA0103.10.582
MA0104.20.959
MA0105.10.021
MA0106.10.0675
MA0107.10.0119
MA0108.22.26836e-4
MA0111.10.715
MA0112.20.00518
MA0113.10.525
MA0114.12.50348e-5
MA0115.10.00154
MA0116.10.139
MA0117.10.982
MA0119.10.174
MA0122.10.883
MA0124.10.716
MA0125.10.252
MA0131.10.247
MA0135.10.806
MA0136.11.15751e-11
MA0137.20.153
MA0138.25.96329e-6
MA0139.10.783
MA0140.10.00185
MA0141.10.211
MA0142.10.0174
MA0143.10.442
MA0144.10.0461
MA0145.10.178
MA0146.10.0436
MA0147.10.877
MA0148.10.0103
MA0149.10.753
MA0150.10.344
MA0152.10.0234
MA0153.15.60953e-7
MA0154.10.0667
MA0155.10.535
MA0156.15.96345e-12
MA0157.10.158
MA0159.10.0511
MA0160.10.175
MA0162.10.305
MA0163.10.00338
MA0164.10.846
MA0258.10.094
MA0259.10.767



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: CNhs12631

Novel motifP-value
10.346
100.0723
1000.243
1010.391
1020.62
1030.295
1040.975
1050.494
1060.0607
1070.361
1080.41
1090.0158
110.272
1100.0732
1110.725
1120.0229
1130.387
1140.901
1150.644
1160.416
1170.00138
1180.599
1190.375
120.908
1200.683
1210.489
1220.975
1232.10001e-5
1240.0333
1250.186
1260.076
1270.605
1280.126
1290.371
134.08607e-10
1300.216
1310.448
1320.618
1330.838
1340.0199
1350.0444
1360.0889
1370.751
1380.645
1390.732
140.463
1400.366
1410.885
1420.351
1430.797
1440.932
1459.90991e-6
1460.363
1470.112
1480.55
1490.644
150.405
1500.0457
1510.759
1520.0857
1530.774
1540.435
1550.478
1560.00986
1570.0402
1580.298
1590.62
1600.377
1610.423
1620.366
1630.953
1640.0355
1650.422
1660.351
1670.776
1680.88
1690.00634
170.108
180.342
190.149
20.352
200.00368
210.195
220.169
230.893
240.0291
250.944
261.37344e-9
270.113
280.917
290.0449
30.13
300.796
310.423
320.853
330.0935
340.993
350.294
360.292
370.0213
380.635
390.326
40.372
400.0816
410.88
420.285
430.207
440.952
450.685
460.0701
470.773
480.573
490.396
50.386
500.173
510.825
520.368
530.361
540.923
550.7
560.605
570.959
580.465
590.395
60.968
600.0466
610.0409
620.37
630.264
640.924
650.552
660.751
670.86
680.878
690.71
70.0186
700.384
710.00167
720.521
730.0325
740.911
750.0701
760.249
770.765
780.00144
790.0635
80.138
800.659
810.415
820.458
830.35
840.569
850.455
860.196
870.436
880.516
890.85
90.547
900.506
910.142
920.893
930.256
940.956
950.0323
960.66
970.747
980.689
990.633



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: CNhs12631


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)
0002610 (raphe nuclei neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0004684 (raphe nuclei)
0001016 (nervous system)
0002275 (reticular formation)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000205 (mouse raphe nuclei neuron 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11722-123D3&oldid=4576677"