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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005149
|DRA_sample_Accession=CAGE@SAMD00005149
|accession_numbers=CAGE;DRX008862;DRR009734;DRZ001159;DRZ002544
|accession_numbers=CAGE;DRX008862;DRR009734;DRZ001159;DRZ002544;DRZ012509;DRZ013894
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0002005,UBERON:0001016
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0002005,UBERON:0001016
|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_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

Revision as of 21:15, 10 August 2017


Name:neurospheres - enteric neuron derived, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13087
Sample type:primary cells
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 numberEN1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005149
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13087 CAGE DRX008862 DRR009734
Accession ID Mm9

Library idBAMCTSS
CNhs13087 DRZ001159 DRZ002544
Accession ID Mm10

Library idBAMCTSS
CNhs13087 DRZ012509 DRZ013894
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

CNhs13087

00
10.0166
100
1000
1000-0.0121
1001-0.0749
1002-0.0644
1003-0.089
10040
1005-0.0219
1006-0.071
1007-0.194
10080
1009-0.0572
1010.0135
10100
1011-0.215
10120
1013-0.0031
10140.119
10150.159
10160.354
10170
10180
10190
1020
10200.289
10210.119
1022-0.251
10230
1024-0.188
1025-0.0417
10260
10270.619
10280
1029-0.1
103-0.0528
10300
10310.369
1032-0.0575
10330.0488
10340
10350
10360.0451
10370
10380.0127
1039-0.151
1040
10400.0916
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: CNhs13087

Jaspar motifP-value
MA0002.24.33091e-5
MA0003.10.0151
MA0004.10.65
MA0006.10.407
MA0007.10.457
MA0009.10.0294
MA0014.10.828
MA0017.16.14993e-5
MA0018.20.00683
MA0019.10.15
MA0024.17.07538e-4
MA0025.10.277
MA0027.10.19
MA0028.10.388
MA0029.10.321
MA0030.10.274
MA0031.10.0581
MA0035.20.00337
MA0038.10.0266
MA0039.20.125
MA0040.10.803
MA0041.10.572
MA0042.10.532
MA0043.10.112
MA0046.11.21583e-9
MA0047.20.00126
MA0048.10.997
MA0050.10.00783
MA0051.10.0277
MA0052.11.10125e-5
MA0055.10.645
MA0057.10.129
MA0058.10.325
MA0059.10.756
MA0060.17.36756e-7
MA0061.10.0457
MA0062.20.993
MA0065.21.81272e-5
MA0066.10.322
MA0067.10.625
MA0068.10.0237
MA0069.10.377
MA0070.10.0952
MA0071.10.409
MA0072.10.457
MA0073.10.876
MA0074.10.762
MA0076.10.282
MA0077.10.0333
MA0078.10.256
MA0079.20.955
MA0080.24.13058e-10
MA0081.10.611
MA0083.10.74
MA0084.10.461
MA0087.10.637
MA0088.10.99
MA0090.10.975
MA0091.10.922
MA0092.10.973
MA0093.10.568
MA0099.20.0745
MA0100.10.492
MA0101.10.346
MA0102.20.583
MA0103.15.91639e-4
MA0104.20.714
MA0105.17.31107e-4
MA0106.10.225
MA0107.10.153
MA0108.20.119
MA0111.10.829
MA0112.27.37614e-6
MA0113.10.182
MA0114.12.16519e-4
MA0115.10.0182
MA0116.10.00114
MA0117.10.768
MA0119.10.0865
MA0122.10.813
MA0124.10.773
MA0125.10.324
MA0131.10.402
MA0135.10.143
MA0136.14.15299e-6
MA0137.20.687
MA0138.20.115
MA0139.10.0959
MA0140.11.44815e-4
MA0141.10.0118
MA0142.10.0685
MA0143.10.215
MA0144.10.333
MA0145.10.0429
MA0146.10.408
MA0147.10.99
MA0148.10.00469
MA0149.10.468
MA0150.10.0815
MA0152.10.229
MA0153.18.21048e-10
MA0154.10.00522
MA0155.10.428
MA0156.10.00115
MA0157.10.0359
MA0159.10.155
MA0160.10.066
MA0162.10.348
MA0163.10.00411
MA0164.10.573
MA0258.10.00873
MA0259.10.642



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: CNhs13087

Novel motifP-value
10.168
100.095
1000.676
1010.569
1020.613
1030.194
1040.878
1050.0408
1060.0327
1070.0606
1080.861
1090.0826
110.178
1100.182
1110.00579
1120.026
1130.405
1140.0307
1150.397
1160.632
1170.5
1180.447
1190.0527
120.605
1200.538
1210.0737
1220.21
1230.315
1240.297
1250.665
1260.621
1270.091
1280.0231
1290.212
130.0539
1300.769
1310.856
1320.353
1330.7
1340.969
1350.768
1360.904
1370.522
1380.596
1390.0741
140.348
1400.00323
1410.204
1420.703
1430.757
1440.773
1450.47
1460.552
1470.794
1480.342
1490.107
150.127
1500.416
1510.295
1520.101
1530.898
1540.719
1550.874
1564.36168e-12
1570.53
1580.346
1590.0306
1600.0972
1610.315
1620.758
1630.9
1640.12
1650.116
1660.837
1670.536
1680.462
1690.0157
170.0409
180.713
190.176
20.371
200.814
210.269
220.314
230.203
240.193
250.471
260.0719
270.29
280.271
290.718
30.157
300.454
310.674
320.0592
330.658
340.367
350.965
360.994
370.0663
380.259
390.498
40.54
400.606
410.582
420.368
430.194
440.163
450.251
460.272
470.242
480.161
490.144
50.255
500.607
510.587
520.331
530.295
540.477
550.938
560.577
570.706
580.115
590.0273
60.701
600.0855
610.317
620.0604
630.101
640.522
650.146
660.41
670.747
680.453
690.865
70.123
700.00144
710.176
720.309
730.217
740.84
750.197
760.976
770.176
780.0617
790.176
80.246
800.537
810.628
820.0121
830.273
840.4
850.131
860.241
870.436
880.618
890.0831
90.406
900.844
910.408
920.153
930.565
940.521
950.238
960.661
970.499
980.0896
990.292



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: CNhs13087


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)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0002005 (enteric 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)
0011142 (mouse neurospheres - enteric 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
CL:0000133 (neurectodermal cell)
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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