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|is_obsolete=
|is_obsolete=
|library_id=CNhs12110
|library_id=CNhs12110
|library_ids=CNhs12110
|name=Mouse Neurons - hippocampal, donor3
|name=Mouse Neurons - hippocampal, donor3
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:41, 25 October 2013


Name:Mouse Neurons - hippocampal, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12110
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 numberRNAMNh3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008729
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12110 CAGE DRX008839 DRR009711
Accession ID Mm9

Library idBAMCTSS
CNhs12110 DRZ001136 DRZ002521
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

CNhs12110

00
10.277
100
1000.575
1000-0.0355
1001-0.0749
10020.511
10030.191
10040
1005-0.384
10060.064
1007-0.0794
10080
1009-0.2
101-0.128
10100
10110.176
10120
1013-0.217
1014-0.0851
10150.396
10160.311
10170
10180
10190
1020
10200.922
10210.283
1022-0.124
10230
1024-0.277
1025-0.0611
10260
10270.392
10280
1029-0.148
103-0.0861
10300
1031-0.458
1032-0.177
10330
10340
10350
1036-0.0378
10370
10380.111
1039-0.338
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: CNhs12110

Jaspar motifP-value
MA0002.20.0275
MA0003.10.136
MA0004.10.87
MA0006.10.0675
MA0007.10.283
MA0009.10.841
MA0014.10.387
MA0017.15.25118e-5
MA0018.20.0328
MA0019.10.0977
MA0024.10.0834
MA0025.10.272
MA0027.10.797
MA0028.10.67
MA0029.10.91
MA0030.10.054
MA0031.10.0191
MA0035.20.221
MA0038.10.15
MA0039.20.00334
MA0040.10.887
MA0041.10.206
MA0042.10.507
MA0043.10.0735
MA0046.16.09893e-9
MA0047.25.81977e-4
MA0048.10.63
MA0050.11.65737e-10
MA0051.18.18298e-5
MA0052.10.0261
MA0055.10.768
MA0057.10.0774
MA0058.10.762
MA0059.10.954
MA0060.16.24941e-6
MA0061.10.0331
MA0062.20.23
MA0065.21.40217e-4
MA0066.10.387
MA0067.10.879
MA0068.10.375
MA0069.10.119
MA0070.10.446
MA0071.10.539
MA0072.10.234
MA0073.10.813
MA0074.10.768
MA0076.10.645
MA0077.14.06695e-5
MA0078.16.0696e-4
MA0079.20.542
MA0080.21.72666e-10
MA0081.10.347
MA0083.13.89726e-5
MA0084.10.634
MA0087.10.623
MA0088.10.303
MA0090.10.00575
MA0091.10.82
MA0092.10.302
MA0093.10.823
MA0099.28.12468e-5
MA0100.10.605
MA0101.10.0396
MA0102.20.339
MA0103.10.163
MA0104.20.234
MA0105.10.0983
MA0106.10.108
MA0107.10.0232
MA0108.20.00799
MA0111.10.981
MA0112.27.50073e-4
MA0113.10.42
MA0114.19.00665e-5
MA0115.10.0652
MA0116.10.238
MA0117.10.623
MA0119.10.136
MA0122.10.682
MA0124.10.879
MA0125.10.287
MA0131.10.948
MA0135.10.34
MA0136.11.61246e-8
MA0137.20.0216
MA0138.20.227
MA0139.10.38
MA0140.10.0212
MA0141.10.0619
MA0142.11.7405e-4
MA0143.12.0373e-4
MA0144.10.0165
MA0145.10.0282
MA0146.10.0816
MA0147.10.258
MA0148.16.17297e-6
MA0149.10.163
MA0150.10.0678
MA0152.10.411
MA0153.12.66988e-8
MA0154.10.0241
MA0155.10.596
MA0156.17.80708e-7
MA0157.10.0298
MA0159.10.0132
MA0160.10.138
MA0162.10.394
MA0163.10.018
MA0164.10.911
MA0258.10.0261
MA0259.10.264



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: CNhs12110

Novel motifP-value
10.275
100.147
1000.948
1010.918
1020.963
1030.29
1040.979
1050.136
1060.00435
1070.0208
1080.509
1090.00409
110.186
1100.176
1110.0462
1120.00166
1130.795
1140.541
1150.153
1160.635
1170.114
1180.467
1190.269
120.48
1200.848
1210.188
1220.39
1230.343
1240.158
1250.185
1260.0931
1270.127
1280.0306
1290.238
132.64717e-6
1300.972
1310.517
1320.813
1330.227
1340.316
1350.277
1360.0297
1370.183
1380.486
1390.366
140.589
1400.998
1410.418
1420.0669
1430.743
1440.835
1450.0699
1460.313
1470.799
1480.478
1490.143
150.217
1500.172
1510.456
1520.0323
1530.903
1540.979
1550.508
1560.0451
1570.011
1580.545
1590.0801
1600.251
1610.357
1620.975
1630.162
1640.0513
1650.0216
1660.624
1670.672
1680.815
1690.0102
170.0192
180.52
190.0522
20.536
200.827
210.704
220.0553
230.285
240.0522
250.822
265.14923e-4
270.778
280.345
290.296
30.131
300.45
310.762
320.57
330.276
340.584
350.177
360.971
370.00809
380.666
390.125
40.742
400.425
410.707
420.521
430.185
440.907
450.37
460.205
470.313
480.231
490.272
50.217
500.158
510.62
520.0451
530.52
540.674
550.595
560.3
570.864
580.304
590.0748
60.67
600.00556
610.532
620.171
630.161
640.573
650.712
660.56
670.743
680.588
690.624
70.0242
700.0717
710.0227
720.383
730.0116
740.534
750.0953
760.957
770.167
780.0304
790.71
80.461
800.79
810.339
820.0567
830.129
840.452
850.0465
860.293
870.174
880.27
890.301
90.434
900.416
910.428
920.201
930.134
940.819
950.0847
960.796
970.965
980.967
990.227



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: CNhs12110


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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