Personal tools

FF:11550-120C2

From FANTOM5_SSTAR

Revision as of 19:53, 31 July 2014 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:Mouse Astrocytes - cerebellar, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12076
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecerebellum
dev stageNA
sexNA
ageNA
cell typeastrocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:3221
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005740
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12076 CAGE DRX008807 DRR009679
Accession ID Mm9

Library idBAMCTSS
CNhs12076 DRZ001104 DRZ002489
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

CNhs12076

00
10
100
1000.0445
10000.612
1001-0.0749
10020.141
10030.387
10040
1005-0.0389
10060.0759
1007-0.304
10080
10090.0822
101-0.443
10100
1011-0.0219
10120
10130.103
10140.131
10150.281
10160.179
10170
10180
10190
1020
10200.558
10210.17
10220.0857
10230
10240
10250
10260
10270.363
10280
1029-0.176
1030.119
10300
10310.113
10320.677
10330
10340
10350
1036-0.045
10370
1038-0.00209
10390.048
1040
10400.381
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: CNhs12076

Jaspar motifP-value
MA0002.20.803
MA0003.10.398
MA0004.10.709
MA0006.10.406
MA0007.10.16
MA0009.10.371
MA0014.10.888
MA0017.10.0114
MA0018.20.636
MA0019.10.527
MA0024.10.55
MA0025.10.954
MA0027.10.729
MA0028.10.0756
MA0029.10.564
MA0030.10.81
MA0031.10.451
MA0035.20.057
MA0038.11
MA0039.20.767
MA0040.10.456
MA0041.10.189
MA0042.10.616
MA0043.10.255
MA0046.13.69195e-6
MA0047.20.437
MA0048.10.321
MA0050.10.00356
MA0051.10.0404
MA0052.10.384
MA0055.10.0378
MA0057.10.779
MA0058.10.933
MA0059.10.246
MA0060.10.00163
MA0061.10.549
MA0062.26.97039e-6
MA0065.20.997
MA0066.10.699
MA0067.10.537
MA0068.10.33
MA0069.10.0565
MA0070.10.524
MA0071.10.731
MA0072.10.838
MA0073.10.752
MA0074.10.61
MA0076.10.0244
MA0077.10.0331
MA0078.10.079
MA0079.20.12
MA0080.21.94472e-7
MA0081.10.0985
MA0083.10.139
MA0084.10.247
MA0087.10.298
MA0088.10.7
MA0090.10.00155
MA0091.10.277
MA0092.10.634
MA0093.10.844
MA0099.20.13
MA0100.10.379
MA0101.10.0661
MA0102.20.0608
MA0103.10.081
MA0104.20.67
MA0105.10.341
MA0106.10.64
MA0107.10.0162
MA0108.20.848
MA0111.10.687
MA0112.20.734
MA0113.10.272
MA0114.10.0152
MA0115.10.232
MA0116.10.788
MA0117.10.614
MA0119.10.153
MA0122.10.668
MA0124.10.443
MA0125.10.985
MA0131.10.114
MA0135.10.639
MA0136.13.22364e-8
MA0137.20.298
MA0138.20.77
MA0139.10.934
MA0140.11.70136e-4
MA0141.10.278
MA0142.10.322
MA0143.10.153
MA0144.10.2
MA0145.10.282
MA0146.10.0166
MA0147.10.568
MA0148.10.19
MA0149.10.388
MA0150.10.974
MA0152.10.215
MA0153.12.97743e-4
MA0154.10.906
MA0155.10.241
MA0156.11.01268e-10
MA0157.10.428
MA0159.10.872
MA0160.10.76
MA0162.10.0444
MA0163.10.441
MA0164.10.743
MA0258.10.712
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: CNhs12076

Novel motifP-value
10.487
100.452
1000.598
1010.707
1020.636
1030.0956
1040.569
1050.893
1060.145
1070.878
1080.383
1090.0158
110.323
1100.626
1110.104
1120.097
1130.351
1140.515
1150.982
1160.174
1170.249
1180.293
1190.258
120.677
1200.713
1210.545
1220.231
1230.762
1240.722
1250.196
1260.509
1270.951
1280.85
1290.487
130.29
1300.793
1310.268
1320.0469
1330.182
1340.684
1350.251
1360.099
1370.169
1380.907
1390.15
140.38
1400.0343
1410.155
1420.0901
1430.186
1440.396
1450.474
1460.96
1470.727
1480.25
1490.64
150.61
1500.312
1510.912
1520.0186
1530.0546
1540.342
1550.502
1560.0175
1570.187
1580.0491
1590.0512
1600.346
1610.851
1620.693
1630.302
1647.58218e-5
1650.509
1660.623
1670.193
1680.544
1690.255
170.851
180.468
190.586
20.143
200.681
210.536
220.137
230.0499
240.636
250.517
260.257
270.533
280.241
290.883
30.787
300.482
310.402
320.293
330.783
340.0673
350.815
360.983
370.527
380.633
390.318
40.88
400.273
410.822
420.897
430.703
440.259
450.453
460.109
470.961
480.676
490.0901
50.119
500.21
510.252
520.225
530.719
540.342
550.409
560.468
570.27
580.0686
590.0831
60.968
600.245
610.619
620.304
630.0618
640.093
650.021
660.188
670.693
680.727
690.592
70.0611
700.568
710.487
720.451
730.0253
740.112
750.407
760.0645
770.0561
785.3338e-4
790.826
80.307
800.562
810.898
820.39
830.888
840.227
850.0499
860.732
873.6079e-4
880.28
890.671
90.623
900.903
910.828
920.399
930.0322
940.177
950.00139
960.338
970.824
980.0752
990.158



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: CNhs12076


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)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)
0002603 (astrocyte of the cerebellum)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002037 (cerebellum)
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)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)
0000196 (mouse astrocyte of cerebellum 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:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11550-120C2&oldid=3271074"