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|rna_weight_ug=10
|rna_weight_ug=10
|sample_age=
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_line=

Revision as of 16:18, 26 December 2012


Name:Mouse Neurons - cortical, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecortex
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 numberRNAMNC1
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

CNhs12112

00
10.185
100
1000.734
10000
1001-0.0749
10020.424
10030.514
10040.0415
1005-0.283
10060.0684
1007-0.00142
10080
1009-0.19
101-0.0884
10100
10110.235
10120
1013-0.217
10140.0829
10150.396
10160.215
10170
10180
10190
1020
10200.461
10210.152
1022-0.124
10230
1024-0.14
10250.0517
10260
10270.413
10280
1029-0.0989
103-0.0787
10300
1031-0.415
1032-0.184
1033-0.00479
10340
10350
1036-0.13
10370
10380.073
1039-0.244
1040
1040-0.155
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: CNhs12112

Jaspar motifP-value
MA0002.20.00327
MA0003.10.105
MA0004.10.905
MA0006.10.104
MA0007.10.338
MA0009.10.586
MA0014.10.389
MA0017.11.40466e-5
MA0018.20.0335
MA0019.10.301
MA0024.10.0804
MA0025.10.233
MA0027.10.796
MA0028.10.993
MA0029.10.389
MA0030.10.613
MA0031.10.115
MA0035.20.0654
MA0038.10.127
MA0039.20.00781
MA0040.10.817
MA0041.10.369
MA0042.10.927
MA0043.10.0326
MA0046.16.28547e-12
MA0047.25.06443e-4
MA0048.10.933
MA0050.11.38617e-9
MA0051.14.87098e-4
MA0052.13.66777e-4
MA0055.10.723
MA0057.10.0777
MA0058.10.729
MA0059.10.889
MA0060.13.69902e-6
MA0061.10.0574
MA0062.20.544
MA0065.22.52739e-5
MA0066.10.216
MA0067.10.942
MA0068.10.135
MA0069.10.048
MA0070.10.413
MA0071.10.241
MA0072.10.116
MA0073.10.849
MA0074.10.368
MA0076.10.396
MA0077.16.53206e-4
MA0078.10.00313
MA0079.20.853
MA0080.22.49737e-10
MA0081.10.465
MA0083.14.78437e-6
MA0084.10.563
MA0087.10.459
MA0088.10.31
MA0090.10.0227
MA0091.10.48
MA0092.10.29
MA0093.10.867
MA0099.22.78736e-5
MA0100.10.64
MA0101.10.19
MA0102.20.857
MA0103.10.0498
MA0104.20.424
MA0105.10.0548
MA0106.10.171
MA0107.10.059
MA0108.20.00167
MA0111.10.763
MA0112.22.80417e-4
MA0113.10.59
MA0114.17.59143e-5
MA0115.10.0341
MA0116.10.0936
MA0117.10.764
MA0119.10.21
MA0122.10.878
MA0124.10.779
MA0125.10.446
MA0131.10.564
MA0135.10.834
MA0136.12.28455e-7
MA0137.20.0854
MA0138.20.824
MA0139.10.128
MA0140.10.00437
MA0141.10.0118
MA0142.10.0113
MA0143.10.00167
MA0144.10.0767
MA0145.10.024
MA0146.10.0978
MA0147.10.409
MA0148.12.70966e-6
MA0149.10.076
MA0150.10.0466
MA0152.10.408
MA0153.19.4975e-11
MA0154.10.0151
MA0155.10.658
MA0156.13.89421e-5
MA0157.10.0193
MA0159.10.00326
MA0160.10.0939
MA0162.10.39
MA0163.10.00401
MA0164.10.991
MA0258.10.0134
MA0259.10.381



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: CNhs12112

Novel motifP-value
10.201
100.207
1000.938
1010.663
1020.718
1030.156
1040.855
1050.414
1060.00847
1070.0317
1080.48
1090.00384
110.148
1100.158
1110.0425
1120.00529
1130.905
1140.276
1150.0853
1160.562
1170.199
1180.64
1190.141
120.547
1200.882
1210.23
1220.365
1230.669
1240.741
1250.53
1260.268
1270.184
1280.0328
1290.155
133.47606e-5
1300.675
1310.64
1320.843
1330.386
1340.562
1350.162
1360.0843
1370.23
1380.696
1390.281
140.568
1400.338
1410.0736
1420.117
1430.798
1440.903
1450.0969
1460.38
1470.94
1480.868
1490.0725
150.258
1500.265
1510.335
1520.0356
1530.794
1540.928
1550.578
1560.00454
1570.163
1580.205
1590.02
1600.372
1610.26
1620.844
1630.0699
1640.0188
1650.00938
1660.587
1670.949
1680.651
1690.00668
170.031
180.784
190.0376
20.448
200.905
210.689
220.0819
230.21
240.0355
250.623
260.00516
270.65
280.334
290.277
30.106
300.439
310.84
320.346
330.244
340.576
350.54
360.693
370.00536
380.382
390.165
40.643
400.201
410.952
420.41
430.146
440.533
450.427
460.283
470.297
480.233
490.19
50.214
500.276
510.563
520.0654
530.495
540.547
550.733
560.297
570.918
580.224
590.0782
60.61
600.00961
610.359
620.132
630.145
640.971
650.357
660.614
670.954
680.919
690.411
70.0284
700.0452
710.0412
720.339
730.0148
740.72
750.154
760.873
770.145
780.0576
790.75
80.318
800.971
810.284
820.0674
830.251
840.962
850.0514
860.236
870.262
880.531
890.163
90.337
900.415
910.353
920.081
930.0781
940.641
950.0416
960.206
970.818
980.663
990.136



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: CNhs12112


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)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
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)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000204 (cortical mouse 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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