Personal tools

FF:630-43F1

From FANTOM5_SSTAR

Revision as of 18:34, 16 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:corpus striatum, neonate N00
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecorpus striatum
dev stage0 day neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008809
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs11226

00
10.452
100
1000.329
10000
1001-0.0668
10020.101
10030.0216
10040
10050
10060.459
10070.0964
10080
1009-0.2
1010.00721
10100
10110.559
10120.329
1013-0.0225
1014-0.0851
10150.338
10160.183
10170
10180
10190
1020
10200
10210
1022-0.103
10230
1024-0.0882
1025-0.0611
10260
10270.479
10280
10290.078
103-0.0887
10300
1031-0.481
1032-0.112
10330
10340
10350
1036-0.131
10370
10380.124
1039-0.178
1040
1040-0.268
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: CNhs11226

Jaspar motifP-value
MA0002.25.96898e-4
MA0003.10.161
MA0004.10.806
MA0006.10.0842
MA0007.10.251
MA0009.10.905
MA0014.10.458
MA0017.13.71339e-6
MA0018.20.00463
MA0019.10.164
MA0024.10.568
MA0025.10.363
MA0027.10.0939
MA0028.10.656
MA0029.10.565
MA0030.10.196
MA0031.10.0196
MA0035.20.0327
MA0038.10.0971
MA0039.20.0254
MA0040.10.157
MA0041.10.86
MA0042.10.612
MA0043.10.0218
MA0046.17.68877e-14
MA0047.22.30883e-6
MA0048.10.351
MA0050.13.39151e-6
MA0051.10.00202
MA0052.10.0133
MA0055.10.266
MA0057.10.127
MA0058.10.7
MA0059.10.538
MA0060.10.0133
MA0061.10.0794
MA0062.20.298
MA0065.29.13215e-6
MA0066.10.125
MA0067.10.548
MA0068.10.6
MA0069.10.119
MA0070.10.524
MA0071.10.134
MA0072.10.124
MA0073.10.664
MA0074.10.285
MA0076.10.709
MA0077.10.153
MA0078.10.289
MA0079.20.638
MA0080.24.96795e-11
MA0081.10.391
MA0083.15.77967e-4
MA0084.10.678
MA0087.10.906
MA0088.10.385
MA0090.10.0187
MA0091.10.248
MA0092.10.199
MA0093.10.824
MA0099.24.35813e-5
MA0100.10.996
MA0101.10.094
MA0102.20.677
MA0103.10.129
MA0104.20.498
MA0105.10.0764
MA0106.10.178
MA0107.10.117
MA0108.21.74017e-4
MA0111.10.926
MA0112.22.37158e-4
MA0113.10.317
MA0114.16.7228e-5
MA0115.10.0013
MA0116.10.0878
MA0117.10.953
MA0119.10.113
MA0122.10.92
MA0124.10.903
MA0125.10.133
MA0131.10.774
MA0135.10.553
MA0136.13.11382e-9
MA0137.20.145
MA0138.20.304
MA0139.10.377
MA0140.15.94122e-4
MA0141.10.00174
MA0142.10.039
MA0143.10.112
MA0144.10.0702
MA0145.10.036
MA0146.10.0409
MA0147.10.609
MA0148.12.55932e-6
MA0149.10.056
MA0150.10.0489
MA0152.10.388
MA0153.12.9665e-12
MA0154.10.0258
MA0155.10.556
MA0156.13.23932e-5
MA0157.10.00864
MA0159.16.49223e-4
MA0160.10.0132
MA0162.10.2
MA0163.10.00403
MA0164.10.902
MA0258.10.00881
MA0259.10.406



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: CNhs11226

Novel motifP-value
10.181
100.149
1000.733
1010.941
1020.941
1030.128
1040.972
1050.167
1060.00628
1070.0338
1080.826
1090.00511
110.0764
1100.0794
1110.128
1120.00433
1130.774
1140.231
1150.723
1160.383
1170.0732
1180.582
1190.189
120.702
1200.859
1210.422
1220.979
1230.305
1240.476
1250.648
1260.141
1270.0865
1280.015
1290.0803
132.89775e-5
1300.801
1310.361
1320.843
1330.584
1340.228
1350.985
1360.0622
1370.548
1380.913
1390.21
140.606
1400.224
1410.174
1420.206
1430.528
1440.846
1450.0182
1460.286
1470.903
1480.356
1490.101
150.154
1500.124
1510.419
1520.0465
1530.803
1540.994
1550.421
1560.0402
1570.26
1580.356
1590.96
1600.155
1610.126
1620.961
1630.382
1640.0803
1650.00516
1660.513
1670.365
1680.355
1690.00566
170.0184
181
190.0339
20.616
200.559
210.412
220.0795
230.226
240.0247
250.681
263.97978e-5
270.699
280.559
290.112
30.11
300.733
310.727
320.342
330.279
340.541
350.675
360.584
370.0166
380.414
390.184
40.538
400.199
410.659
420.342
430.131
440.446
450.47
460.173
470.213
480.181
490.202
50.164
500.231
510.621
520.101
530.76
540.602
550.8
560.338
570.726
580.285
590.0364
60.851
600.0157
610.181
620.141
630.101
640.725
650.227
660.991
670.471
680.909
690.519
70.0358
700.0312
710.0165
720.359
730.0223
740.388
750.12
760.933
770.163
780.00897
790.746
80.149
800.975
810.517
820.0787
830.0172
840.776
850.0402
860.26
870.0493
880.257
890.391
90.364
900.341
910.114
920.239
930.0361
940.855
950.0615
960.336
970.998
980.612
990.15



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: CNhs11226


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
0000479 (tissue)
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)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011392 (mouse corpus striatum- neonate N00 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
UBERON:0010082 (future corpus striatum)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:630-43F1&oldid=3076626"