Personal tools

FF:11807-124D7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000073,UBERON:0002410,UBERON:0004121,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0000010,UBERON:0000011,UBERON:0001016,UBERON:0000924,UBERON:0005743,UBERON:0006601
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0000011,UBERON:0001016
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0000107,CL:0000133
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0000107
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0011143
|comment=
|comment=
|created_by=
|created_by=

Revision as of 22:07, 4 July 2012


Name:neurospheres - parasympathetic neuron derived, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberpara1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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

CNhs13084

00
10
100
1000
1000-0.0355
1001-0.0356
1002-0.0986
1003-0.102
10040
1005-0.0389
1006-0.09
1007-0.0036
10080
1009-0.0572
1010.0203
10100
1011-0.0145
10120
1013-0.066
10140
10150.133
10160.447
10170
10180
10190
1020
10200.386
10210.0931
1022-0.284
10230
10240
1025-0.0611
10260
10270.341
10280.0931
1029-0.0217
103-0.0754
10300
10310.377
1032-0.052
10330.17
10340
10350
10360.0254
10370
10380
1039-0.293
1040
10400.148
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: CNhs13084

Jaspar motifP-value
MA0002.20.00104
MA0003.10.00807
MA0004.10.619
MA0006.10.387
MA0007.10.852
MA0009.10.0336
MA0014.10.669
MA0017.13.63867e-5
MA0018.20.00971
MA0019.10.974
MA0024.10.00149
MA0025.10.747
MA0027.10.732
MA0028.10.114
MA0029.10.279
MA0030.10.794
MA0031.10.312
MA0035.20.00228
MA0038.10.307
MA0039.20.296
MA0040.10.978
MA0041.10.0809
MA0042.10.658
MA0043.10.163
MA0046.13.34815e-18
MA0047.20.00213
MA0048.10.809
MA0050.10.0183
MA0051.10.0273
MA0052.10.00363
MA0055.10.663
MA0057.10.19
MA0058.10.281
MA0059.10.554
MA0060.11.72033e-6
MA0061.10.0368
MA0062.20.14
MA0065.22.3043e-5
MA0066.10.216
MA0067.10.489
MA0068.10.41
MA0069.10.508
MA0070.10.115
MA0071.10.263
MA0072.10.286
MA0073.10.986
MA0074.10.973
MA0076.10.0555
MA0077.10.00516
MA0078.10.074
MA0079.20.276
MA0080.25.49205e-7
MA0081.10.975
MA0083.10.0915
MA0084.10.8
MA0087.10.517
MA0088.10.725
MA0090.10.568
MA0091.10.691
MA0092.10.627
MA0093.10.506
MA0099.20.459
MA0100.10.28
MA0101.10.329
MA0102.20.297
MA0103.12.28132e-4
MA0104.20.859
MA0105.11.94939e-5
MA0106.10.0925
MA0107.10.0978
MA0108.27.21559e-4
MA0111.10.973
MA0112.24.46611e-5
MA0113.10.551
MA0114.17.84356e-5
MA0115.10.113
MA0116.12.45625e-4
MA0117.10.654
MA0119.10.0595
MA0122.10.731
MA0124.10.585
MA0125.10.21
MA0131.10.341
MA0135.10.778
MA0136.10.00196
MA0137.20.381
MA0138.20.00616
MA0139.10.0249
MA0140.10.00132
MA0141.10.0218
MA0142.10.147
MA0143.10.06
MA0144.10.857
MA0145.10.0893
MA0146.10.893
MA0147.10.843
MA0148.10.0128
MA0149.10.295
MA0150.10.218
MA0152.10.89
MA0153.17.31059e-13
MA0154.10.00169
MA0155.10.577
MA0156.10.0305
MA0157.10.122
MA0159.10.397
MA0160.10.121
MA0162.10.318
MA0163.10.00589
MA0164.10.886
MA0258.10.0268
MA0259.10.992



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: CNhs13084

Novel motifP-value
10.145
100.136
1000.821
1010.768
1020.914
1030.0815
1040.884
1050.0573
1060.0117
1070.0325
1080.918
1090.104
110.116
1100.3
1110.0101
1120.0399
1130.453
1140.035
1150.456
1160.711
1170.664
1180.623
1190.0621
120.479
1200.696
1210.252
1220.44
1230.678
1240.578
1250.644
1260.253
1270.462
1280.00834
1290.0928
130.155
1300.679
1310.547
1320.145
1330.464
1340.819
1350.47
1360.653
1370.361
1380.254
1390.0688
140.39
1400.00292
1410.0818
1420.937
1430.668
1440.805
1450.357
1460.424
1470.854
1480.585
1490.272
150.126
1500.518
1510.374
1520.0973
1530.583
1540.616
1550.863
1560.368
1570.512
1580.736
1590.366
1600.181
1610.602
1620.909
1630.823
1640.139
1650.258
1660.478
1670.549
1680.704
1690.0238
170.0686
180.728
190.0814
20.326
200.997
210.36
220.563
230.345
240.415
250.347
260.0502
270.26
280.437
290.931
30.101
300.519
310.69
320.0779
330.471
340.357
350.602
360.689
370.126
380.366
390.437
40.877
400.428
410.987
420.282
430.197
440.309
450.33
460.197
470.169
480.206
490.135
50.209
500.81
510.51
520.211
530.323
540.461
550.983
560.557
570.484
580.0617
590.0381
60.855
600.0898
610.645
620.0211
630.15
640.395
650.23
660.431
670.792
680.505
690.734
70.126
700.0172
710.193
720.421
730.288
740.172
750.338
760.963
770.229
780.132
790.327
80.146
800.717
810.474
820.0198
830.125
840.735
850.0673
860.372
870.35
880.512
890.0307
90.357
900.742
910.288
920.0436
930.53
940.264
950.294
960.252
970.622
980.168
990.186



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: CNhs13084


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)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0000011 (parasympathetic nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011143 (mouse neurospheres - parasympathetic neuron derived 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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11807-124D7&oldid=1845721"