Personal tools

FF:11724-123D5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:11724-123D5
|id=FF:11724-123D5
|name=Mouse Neurons - substantia nigra, donor1
|name=Mouse Neurons - cortical, donor1
|sample_id=11724
|sample_id=11724
|rna_tube_id=123D5
|rna_tube_id=123D5
Line 14: Line 14:
|sample_strain=
|sample_strain=
|sample_dev_stage=
|sample_dev_stage=
|sample_tissue=substantia nigra
|sample_tissue=cortex
|sample_donor(cell lot)=
|sample_donor(cell lot)=
|sample_sex=
|sample_sex=
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10.00000
|rna_weight_ug=10
|rna_concentration=1.46000
|rna_concentration=1.46
|sample_note=
|sample_note=was originally substantia nigra, sample provider error
|profile_hcage=CNhs12025,LSID837,release011,COMPLETED
|profile_hcage=CNhs12025,LSID837,release011,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,

Revision as of 17:48, 27 February 2012


Name:Mouse Neurons - cortical, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
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 numberRNAMNC2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12025

00
10.189
100
1000.767
1000-0.0157
1001-0.0631
10020.46
10030.537
10040.0428
1005-0.282
10060.0527
10070.0592
10080
1009-0.2
101-0.0748
10100
10110.0739
10120.0428
1013-0.184
10140.118
10150.426
10160.249
10170
10180
10190
1020
10200.389
10210.118
1022-0.124
10230
1024-0.14
10250
10260
10270.568
10280
1029-0.101
103-0.0719
10300
1031-0.477
1032-0.177
1033-0.0236
10340
10350
1036-0.12
10370
10380.186
1039-0.231
1040
1040-0.173
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 no result for this sample


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: CNhs12025

Jaspar motifP-value
MA0002.20.00258
MA0003.10.0931
MA0004.10.835
MA0006.10.132
MA0007.10.348
MA0009.10.683
MA0014.10.402
MA0017.11.17954e-5
MA0018.20.053
MA0019.10.347
MA0024.10.0552
MA0025.10.214
MA0027.10.754
MA0028.10.915
MA0029.10.419
MA0030.10.417
MA0031.10.0713
MA0035.20.0417
MA0038.10.106
MA0039.20.0152
MA0040.10.581
MA0041.10.314
MA0042.10.996
MA0043.10.0356
MA0046.11.4892e-14
MA0047.22.86339e-4
MA0048.10.882
MA0050.11.1127e-8
MA0051.10.00103
MA0052.15.49273e-5
MA0055.10.664
MA0057.10.0799
MA0058.10.692
MA0059.10.685
MA0060.11.67427e-6
MA0061.10.0734
MA0062.20.639
MA0065.21.54522e-5
MA0066.10.2
MA0067.10.782
MA0068.10.212
MA0069.10.0436
MA0070.10.449
MA0071.10.208
MA0072.10.111
MA0073.10.703
MA0074.10.302
MA0076.10.33
MA0077.10.00362
MA0078.10.00675
MA0079.20.936
MA0080.22.16772e-11
MA0081.10.489
MA0083.16.59244e-6
MA0084.10.657
MA0087.10.673
MA0088.10.306
MA0090.10.0195
MA0091.10.404
MA0092.10.318
MA0093.10.829
MA0099.21.11985e-5
MA0100.10.641
MA0101.10.247
MA0102.20.963
MA0103.10.0481
MA0104.20.528
MA0105.10.0431
MA0106.10.22
MA0107.10.133
MA0108.28.82552e-5
MA0111.10.742
MA0112.21.40191e-4
MA0113.10.483
MA0114.19.61006e-5
MA0115.10.0169
MA0116.10.0675
MA0117.10.871
MA0119.10.175
MA0122.10.814
MA0124.10.995
MA0125.10.404
MA0131.10.554
MA0135.10.717
MA0136.12.35308e-8
MA0137.20.0789
MA0138.20.743
MA0139.10.134
MA0140.10.00444
MA0141.10.00651
MA0142.10.0079
MA0143.10.00177
MA0144.10.0577
MA0145.10.0194
MA0146.10.0867
MA0147.10.584
MA0148.11.37487e-6
MA0149.10.0558
MA0150.10.0388
MA0152.10.42
MA0153.12.73981e-12
MA0154.10.0154
MA0155.10.591
MA0156.14.86293e-5
MA0157.10.0136
MA0159.10.00227
MA0160.10.057
MA0162.10.337
MA0163.10.00336
MA0164.10.92
MA0258.10.00595
MA0259.10.476



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: CNhs12025

Novel motifP-value
10.207
100.202
1000.981
1010.704
1020.703
1030.119
1040.896
1050.433
1060.00943
1070.0511
1080.644
1090.00341
110.134
1100.176
1110.0423
1120.00557
1130.907
1140.236
1150.11
1160.463
1170.164
1180.647
1190.104
120.535
1200.8
1210.135
1220.402
1230.685
1240.923
1250.325
1260.235
1270.133
1280.0227
1290.172
131.27472e-4
1300.738
1310.436
1320.705
1330.526
1340.531
1350.184
1360.109
1370.294
1380.782
1390.234
140.581
1400.508
1410.0418
1420.157
1430.579
1440.765
1450.0852
1460.34
1470.992
1480.78
1490.0486
150.236
1500.309
1510.331
1520.0359
1530.945
1540.978
1550.574
1560.00127
1570.16
1580.254
1590.0954
1600.327
1610.242
1620.989
1630.0834
1640.0263
1650.00464
1660.588
1670.605
1680.461
1690.00575
170.0285
180.929
190.0442
20.42
200.807
210.542
220.0893
230.195
240.0299
250.553
260.00743
270.596
280.397
290.282
30.0838
300.405
310.768
320.258
330.235
340.488
350.666
360.562
370.00787
380.395
390.225
40.587
400.171
410.773
420.313
430.178
440.495
450.409
460.222
470.21
480.19
490.203
50.173
500.301
510.602
520.0714
530.44
540.532
550.472
560.279
570.932
580.197
590.0466
60.666
600.0137
610.352
620.108
630.142
640.874
650.279
660.728
670.734
680.725
690.256
70.0413
700.0175
710.0426
720.292
730.016
740.427
750.128
760.871
770.126
780.0644
790.899
80.277
800.891
810.28
820.0622
830.0447
840.695
850.0292
860.295
870.203
880.63
890.156
90.335
900.387
910.371
920.091
930.0577
940.643
950.0479
960.238
970.832
980.516
990.194



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: CNhs12025


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000003 (native cell)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000117 (CNS neuron (sensu Vertebrata))
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000125 (neural nucleus)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001891 (midbrain)
0001893 (telencephalon)
0002020 (gray matter)
0002038 (substantia nigra)
0002050 (embryonic structure)
0002298 (brainstem)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0002950 (regional part of midbrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003528 (brain grey matter)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006331 (brainstem nucleus)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11724-123D5&oldid=417307"