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|is_obsolete=
|is_obsolete=
|library_id=CNhs12359
|library_id=CNhs12359
|library_ids=CNhs12359
|name=Mouse Neurons - hippocampal, donor2
|name=Mouse Neurons - hippocampal, donor2
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 16:16, 25 October 2013


Name:Mouse Neurons - hippocampal, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12359
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuehippocampus
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 numberRNAMNh2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008728
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12359 CAGE DRX008838 DRR009710
Accession ID Mm9

Library idBAMCTSS
CNhs12359 DRZ001135 DRZ002520
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

CNhs12359

00
10.197
100
1000.644
1000-0.0172
1001-0.0749
10020.331
10030.0693
10040.0397
1005-0.193
10060.158
10070.0694
10080
1009-0.2
101-0.12
10100
10110.133
10120
1013-0.177
10140
10150.401
10160.105
10170
10180
10190
1020
10200.519
10210.197
1022-0.124
10230
1024-0.166
1025-0.0611
10260
10270.506
10280
1029-0.143
103-0.0829
10300
1031-0.511
1032-0.184
10330.00967
10340
10350
1036-0.0917
10370
10380.1
1039-0.272
1040
1040-0.176
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: CNhs12359

Jaspar motifP-value
MA0002.20.00184
MA0003.10.123
MA0004.10.791
MA0006.10.0762
MA0007.10.209
MA0009.10.85
MA0014.10.291
MA0017.11.12608e-5
MA0018.20.0176
MA0019.10.316
MA0024.10.00552
MA0025.10.228
MA0027.10.713
MA0028.10.667
MA0029.10.695
MA0030.10.263
MA0031.10.0578
MA0035.20.111
MA0038.10.0685
MA0039.20.00464
MA0040.10.976
MA0041.10.303
MA0042.10.66
MA0043.10.0121
MA0046.13.13136e-10
MA0047.25.05943e-4
MA0048.10.948
MA0050.15.6446e-9
MA0051.19.60025e-4
MA0052.18.95073e-4
MA0055.10.847
MA0057.10.0569
MA0058.10.739
MA0059.10.828
MA0060.11.07697e-9
MA0061.10.0561
MA0062.20.991
MA0065.24.10713e-5
MA0066.10.332
MA0067.10.837
MA0068.10.505
MA0069.10.15
MA0070.10.523
MA0071.10.321
MA0072.10.222
MA0073.10.891
MA0074.10.518
MA0076.10.169
MA0077.10.00177
MA0078.10.00513
MA0079.20.707
MA0080.28.40341e-11
MA0081.10.486
MA0083.12.65846e-5
MA0084.10.704
MA0087.10.513
MA0088.10.372
MA0090.10.00817
MA0091.10.501
MA0092.10.207
MA0093.10.785
MA0099.26.63132e-5
MA0100.10.688
MA0101.10.171
MA0102.20.678
MA0103.10.0755
MA0104.20.315
MA0105.10.114
MA0106.10.153
MA0107.10.0914
MA0108.20.0057
MA0111.10.953
MA0112.22.43408e-4
MA0113.10.715
MA0114.11.33087e-4
MA0115.10.0591
MA0116.10.186
MA0117.10.795
MA0119.10.153
MA0122.10.845
MA0124.10.83
MA0125.10.203
MA0131.10.594
MA0135.10.386
MA0136.13.70079e-7
MA0137.20.0853
MA0138.20.776
MA0139.10.228
MA0140.10.00348
MA0141.10.0142
MA0142.10.00435
MA0143.19.71555e-4
MA0144.10.0473
MA0145.10.0154
MA0146.10.0717
MA0147.10.386
MA0148.11.47577e-5
MA0149.10.0648
MA0150.10.0296
MA0152.10.416
MA0153.11.54527e-8
MA0154.10.0284
MA0155.10.723
MA0156.13.50178e-4
MA0157.10.0303
MA0159.10.0046
MA0160.10.0967
MA0162.10.363
MA0163.10.0165
MA0164.10.968
MA0258.10.0119
MA0259.10.368



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: CNhs12359

Novel motifP-value
10.21
100.233
1000.889
1010.912
1020.943
1030.0815
1040.945
1050.306
1060.00294
1070.018
1080.617
1090.00372
110.112
1100.222
1110.0389
1120.00647
1130.831
1140.16
1150.314
1160.584
1170.312
1180.523
1190.175
120.498
1200.825
1210.361
1220.704
1230.726
1240.69
1250.371
1260.245
1270.14
1280.0219
1290.149
132.8111e-5
1300.866
1310.392
1320.961
1330.307
1340.439
1350.126
1360.0654
1370.318
1380.5
1390.131
140.569
1400.425
1410.126
1420.128
1430.761
1440.909
1450.0918
1460.448
1470.885
1480.415
1490.0941
150.201
1500.213
1510.373
1520.0202
1530.837
1540.886
1550.652
1560.00462
1570.183
1580.298
1590.036
1600.3
1610.418
1620.761
1630.144
1640.0314
1650.0109
1660.677
1670.667
1680.589
1690.00734
170.0228
180.697
190.0332
20.47
200.875
210.619
220.0633
230.211
240.0516
250.674
260.00343
270.638
280.386
290.352
30.13
300.449
310.792
320.271
330.353
340.526
350.377
360.848
370.0097
380.422
390.204
40.553
400.294
410.904
420.393
430.177
440.693
450.364
460.194
470.212
480.185
490.218
50.185
500.282
510.552
520.0465
530.484
540.534
550.943
560.319
570.794
580.268
590.0671
60.671
600.0088
610.308
620.162
630.129
640.933
650.372
660.57
670.72
680.662
690.525
70.0418
700.0246
710.0475
720.326
730.0102
740.276
750.151
760.976
770.17
780.0523
790.506
80.271
800.936
810.296
820.0374
830.0456
840.922
850.0364
860.326
870.33
880.449
890.175
90.335
900.392
910.247
920.113
930.0215
940.892
950.0654
960.277
970.838
980.718
990.178



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: CNhs12359


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)
0002609 (neuron of cerebral cortex)
0002608 (hippocampal neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000201 (hippocampal neuron sample)
0000203 (mouse neuron samples)
0000202 (mouse hippocampal 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)

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