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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004728
|DRA_sample_Accession=CAGE@SAMD00004728
|accession_numbers=CAGE;DRX008824;DRR009696;DRZ001121;DRZ002506
|accession_numbers=CAGE;DRX008824;DRR009696;DRZ001121;DRZ002506;DRZ012471;DRZ013856
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0000119,UBERON:0003210
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0000119,UBERON:0003210
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000708
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000708

Revision as of 20:57, 10 August 2017


Name:Mouse Meningeal cells, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12109
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemeninges
dev stageNA
sexNA
ageNA
cell typemeningeal cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAM5771
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004728
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12109 CAGE DRX008824 DRR009696
Accession ID Mm9

Library idBAMCTSS
CNhs12109 DRZ001121 DRZ002506
Accession ID Mm10

Library idBAMCTSS
CNhs12109 DRZ012471 DRZ013856
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

CNhs12109

00
10
100
1000
10000
1001-0.0749
10020.157
10030.101
10040
10050
1006-0.143
1007-0.228
10080
1009-0.0572
101-0.475
10100
1011-0.3
10120
10130.0596
1014-0.0851
10150.114
10160.265
10170
10180
10190
1020
10200.444
10210.444
1022-0.124
10230
1024-0.307
1025-0.0233
10260
1027-0.048
10280
1029-0.176
1030.444
10300
10311.094
1032-0.177
1033-0.0665
10340
10350
1036-0.183
10370
1038-0.0779
1039-0.072
1040
10400.513
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: CNhs12109

Jaspar motifP-value
MA0002.20.0221
MA0003.10.277
MA0004.10.289
MA0006.10.45
MA0007.10.113
MA0009.10.586
MA0014.10.453
MA0017.10.781
MA0018.20.00341
MA0019.10.643
MA0024.10.00334
MA0025.10.188
MA0027.10.742
MA0028.10.0689
MA0029.10.673
MA0030.10.253
MA0031.10.667
MA0035.20.301
MA0038.10.0102
MA0039.20.342
MA0040.10.385
MA0041.10.296
MA0042.10.681
MA0043.10.0144
MA0046.16.44568e-5
MA0047.20.193
MA0048.10.261
MA0050.10.365
MA0051.10.873
MA0052.10.0308
MA0055.10.0927
MA0057.10.142
MA0058.10.216
MA0059.10.164
MA0060.10.0124
MA0061.10.141
MA0062.27.4938e-4
MA0065.20.312
MA0066.10.0676
MA0067.10.284
MA0068.10.816
MA0069.10.7
MA0070.10.824
MA0071.10.552
MA0072.10.147
MA0073.10.689
MA0074.10.0875
MA0076.10.00456
MA0077.10.0337
MA0078.10.165
MA0079.20.474
MA0080.20.00453
MA0081.10.112
MA0083.10.00561
MA0084.10.747
MA0087.10.617
MA0088.10.464
MA0090.10.00146
MA0091.10.744
MA0092.10.0168
MA0093.10.353
MA0099.23.22535e-6
MA0100.10.561
MA0101.10.44
MA0102.20.0378
MA0103.10.0947
MA0104.20.808
MA0105.10.0619
MA0106.10.00236
MA0107.10.88
MA0108.20.587
MA0111.10.567
MA0112.20.00439
MA0113.10.324
MA0114.10.798
MA0115.10.619
MA0116.10.0147
MA0117.10.345
MA0119.10.0861
MA0122.10.809
MA0124.10.285
MA0125.10.257
MA0131.10.225
MA0135.10.92
MA0136.10.00709
MA0137.20.524
MA0138.20.0389
MA0139.10.228
MA0140.10.0271
MA0141.10.105
MA0142.10.811
MA0143.10.603
MA0144.10.777
MA0145.10.0516
MA0146.10.0103
MA0147.10.742
MA0148.10.144
MA0149.10.181
MA0150.10.498
MA0152.10.235
MA0153.10.00644
MA0154.10.0886
MA0155.10.273
MA0156.13.23238e-5
MA0157.10.757
MA0159.10.221
MA0160.10.303
MA0162.10.126
MA0163.10.00397
MA0164.10.918
MA0258.10.0136
MA0259.10.817



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: CNhs12109

Novel motifP-value
10.284
100.309
1000.927
1010.982
1020.417
1030.259
1040.982
1050.59
1060.00924
1070.426
1080.497
1090.00376
110.0187
1100.303
1110.535
1120.201
1130.774
1140.234
1150.834
1160.0164
1170.373
1180.629
1190.0127
120.77
1200.871
1210.664
1220.201
1230.634
1240.195
1250.169
1260.78
1270.0858
1280.0798
1290.53
130.337
1300.288
1310.266
1320.244
1330.905
1340.429
1350.474
1360.492
1370.454
1380.323
1390.535
140.872
1400.963
1410.392
1420.399
1430.0169
1440.473
1450.0248
1460.93
1470.404
1480.627
1490.029
150.631
1500.193
1510.704
1520.0431
1530.333
1540.423
1550.177
1560.0534
1570.258
1580.356
1590.262
1600.382
1610.168
1620.291
1630.432
1640.836
1650.907
1660.324
1670.103
1680.545
1690.0403
170.188
180.103
190.0965
20.19
200.853
210.132
220.0339
230.0619
240.0564
250.357
260.0709
270.581
280.945
290.261
30.19
300.338
310.479
320.0613
330.734
340.156
350.903
360.546
370.0531
380.178
390.272
40.174
400.18
410.52
420.189
430.073
440.04
450.388
460.0822
470.0489
480.398
490.263
50.909
500.158
510.997
520.103
530.989
540.647
550.201
560.302
570.162
580.76
590.014
60.771
600.072
610.973
620.453
630.0835
640.162
650.0154
660.307
670.766
680.942
690.14
70.927
700.0388
710.151
720.636
730.016
740.883
750.176
760.929
770.00931
780.329
790.698
80.109
800.574
810.111
820.398
830.537
840.708
850.0111
860.642
870.025
880.512
890.866
90.694
900.671
910.051
920.18
930.806
940.95
950.0159
960.672
970.388
980.143
990.439



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: CNhs12109


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)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000708 (leptomeningeal cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0000119 (cell layer)
0003210 (blood-cerebrospinal fluid barrier)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000111 (mouse leptomeningeal cell 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:0000134 (mesenchymal cell)

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