Personal tools

FF:11551-120C3

From FANTOM5_SSTAR

Revision as of 18:08, 4 June 2020 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:Mouse Astrocytes - hippocampus, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12077
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuehippocampus
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:3899
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004768
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12077 CAGE DRX008809 DRR009681
Accession ID Mm9

Library idBAMCTSS
CNhs12077 DRZ001106 DRZ002491
Accession ID Mm10

Library idBAMCTSS
CNhs12077 DRZ012456 DRZ013841
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs12077

00
10
100
1000
10000.715
1001-0.0491
10020.44
10030.498
10040
1005-0.00897
10060.019
1007-0.315
10080
10090.333
101-0.377
10100
1011-0.0304
10120
10130.333
1014-0.00795
10150.015
10160.288
10170
10180
10190
1020
10200.672
10210.0772
10220.0693
10230
1024-0.0127
1025-0.0611
10260
10270.0772
10280.143
1029-0.176
1030.188
10300
10310.179
10320.531
1033-0.0385
10340
10350
1036-0.219
10370
10380.137
10390.184
1040
10400.51
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: CNhs12077

Jaspar motifP-value
MA0002.20.906
MA0003.10.232
MA0004.10.831
MA0006.10.244
MA0007.10.131
MA0009.10.582
MA0014.10.444
MA0017.10.0289
MA0018.20.61
MA0019.10.555
MA0024.14.18849e-5
MA0025.10.633
MA0027.10.35
MA0028.10.148
MA0029.10.996
MA0030.10.652
MA0031.10.876
MA0035.20.00599
MA0038.10.372
MA0039.20.176
MA0040.10.499
MA0041.10.157
MA0042.10.557
MA0043.10.275
MA0046.15.7961e-5
MA0047.20.317
MA0048.10.654
MA0050.10.35
MA0051.10.487
MA0052.10.437
MA0055.10.189
MA0057.10.978
MA0058.10.95
MA0059.10.774
MA0060.10.688
MA0061.10.422
MA0062.28.24389e-4
MA0065.20.319
MA0066.10.501
MA0067.10.792
MA0068.10.373
MA0069.10.0338
MA0070.10.781
MA0071.10.389
MA0072.10.536
MA0073.10.781
MA0074.10.836
MA0076.10.2
MA0077.10.491
MA0078.10.852
MA0079.20.00704
MA0080.29.47975e-7
MA0081.10.421
MA0083.10.918
MA0084.10.151
MA0087.10.214
MA0088.10.923
MA0090.17.88658e-5
MA0091.10.0324
MA0092.10.866
MA0093.10.938
MA0099.20.0297
MA0100.10.649
MA0101.10.0653
MA0102.20.486
MA0103.10.0182
MA0104.20.253
MA0105.10.0781
MA0106.10.146
MA0107.10.0418
MA0108.20.53
MA0111.10.673
MA0112.20.768
MA0113.10.658
MA0114.10.00148
MA0115.10.108
MA0116.10.085
MA0117.10.866
MA0119.10.427
MA0122.10.697
MA0124.10.329
MA0125.10.933
MA0131.10.0481
MA0135.10.119
MA0136.11.20481e-6
MA0137.20.84
MA0138.20.508
MA0139.10.391
MA0140.16.74532e-6
MA0141.10.588
MA0142.10.393
MA0143.10.713
MA0144.10.836
MA0145.10.0475
MA0146.10.0205
MA0147.10.184
MA0148.10.115
MA0149.10.839
MA0150.10.94
MA0152.10.454
MA0153.13.19402e-4
MA0154.10.493
MA0155.10.405
MA0156.12.35917e-7
MA0157.10.747
MA0159.10.233
MA0160.10.492
MA0162.10.239
MA0163.10.564
MA0164.10.755
MA0258.10.293
MA0259.10.174



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: CNhs12077

Novel motifP-value
10.134
100.103
1000.468
1010.874
1020.542
1030.106
1040.798
1050.902
1060.234
1070.897
1080.705
1090.0609
110.606
1100.981
1110.214
1120.217
1130.342
1140.772
1150.689
1160.419
1170.0874
1180.101
1190.279
120.976
1200.554
1210.653
1220.439
1230.994
1240.578
1250.625
1260.239
1270.913
1280.92
1290.158
130.187
1300.652
1310.993
1320.247
1330.48
1340.842
1350.387
1360.00965
1370.103
1380.645
1390.487
140.411
1400.00495
1410.588
1420.0871
1430.536
1440.77
1450.49
1460.926
1470.866
1480.332
1490.478
150.779
1500.461
1510.785
1520.00323
1530.0606
1540.219
1550.455
1560.0059
1570.662
1580.0256
1590.0832
1600.133
1610.762
1620.949
1630.219
1640.00292
1650.696
1660.793
1670.0785
1680.326
1690.212
170.958
180.641
190.446
20.049
200.922
210.695
220.122
230.134
240.386
250.288
260.143
270.986
280.526
290.552
30.29
300.246
310.497
320.0435
330.614
340.334
350.324
360.0347
370.323
380.772
390.456
40.947
400.586
410.843
420.606
430.335
440.297
450.24
460.0433
470.958
480.821
490.0395
50.066
500.194
510.149
520.221
530.885
540.39
550.686
560.818
570.879
580.0377
590.13
60.859
600.238
610.6
620.12
630.233
640.865
650.261
660.508
670.982
680.465
690.258
70.233
700.582
710.0403
720.499
730.00303
740.291
750.229
760.161
770.0646
780.0135
790.892
80.407
800.219
810.643
820.778
830.95
840.266
850.338
860.88
872.5117e-4
880.427
890.597
90.376
900.331
910.842
920.36
930.0441
940.0158
950.00691
960.0681
970.825
980.27
990.256



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: CNhs12077


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)
0002605 (astrocyte of the cerebral cortex)
0002604 (astrocyte of the hippocampus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
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)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)
0000197 (mouse astrocyte of hippocampus 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:11551-120C3&oldid=4576557"