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|DRA_sample_Accession=CAGE@SAMD00005583
|DRA_sample_Accession=CAGE@SAMD00005583
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|HumanCAGEScanFiles=NCig10027;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.tissue.CAGEScan/medulla%2520oblongata%252c%2520adult%252c%2520donor10252.NCig10027.10155-103A2.hg19.GCTATA.3prime.fq.gz;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.tissue.CAGEScan/medulla%2520oblongata%252c%2520adult%252c%2520donor10252.NCig10027.10155-103A2.hg19.GCTATA.5prime.fq.gz;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.tissue.CAGEScan/medulla%2520oblongata%252c%2520adult%252c%2520donor10252.NCig10027.10155-103A2.hg19.GCTATA.bam;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.tissue.CAGEScan/medulla%2520oblongata%252c%2520adult%252c%2520donor10252.NCig10027.10155-103A2.hg19.GCTATA.pairs.bed.gz
|accession_numbers=CAGE;DRX008687;DRR009559;DRZ000984;DRZ002369
|accession_numbers=CAGE;DRX008687;DRR009559;DRZ000984;DRZ002369;DRZ012334;DRZ013719
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
Line 64: Line 64:
|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Revision as of 19:03, 10 August 2017

Name:medulla oblongata, adult, donor10252
Species:Human (Homo sapiens)
Library ID:CNhs12315
Sample type:tissues
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemedulla oblongata
dev stageNA
sexfemale
age76
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005583
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12315 CAGE DRX008687 DRR009559
Accession ID Hg19

Library idBAMCTSS
CNhs12315 DRZ000984 DRZ002369
Accession ID Hg38

Library idBAMCTSS
CNhs12315 DRZ012334 DRZ013719
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload
HumanCAGEScan Download raw sequence, BAM & CTSS

Library id3prime-FASTQ5prime-FASTQBAMCTSS
NCig10027downloaddownloaddownloaddownload


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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0.125
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.798
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12315

Jaspar motifP-value
MA0002.20.0152
MA0003.10.213
MA0004.10.282
MA0006.10.54
MA0007.10.398
MA0009.10.0915
MA0014.10.688
MA0017.10.00697
MA0018.20.275
MA0019.10.716
MA0024.10.789
MA0025.10.779
MA0027.10.589
MA0028.10.0467
MA0029.10.03
MA0030.10.0105
MA0031.10.136
MA0035.20.00526
MA0038.10.13
MA0039.20.441
MA0040.10.588
MA0041.10.698
MA0042.10.843
MA0043.10.685
MA0046.10.021
MA0047.20.49
MA0048.10.15
MA0050.10.173
MA0051.10.299
MA0052.10.903
MA0055.10.00289
MA0057.10.819
MA0058.10.364
MA0059.10.068
MA0060.10.102
MA0061.10.00283
MA0062.20.00217
MA0065.27.03251e-4
MA0066.10.00728
MA0067.10.997
MA0068.10.99
MA0069.10.689
MA0070.10.404
MA0071.10.0544
MA0072.10.617
MA0073.10.506
MA0074.10.214
MA0076.10.0965
MA0077.10.0465
MA0078.10.868
MA0079.20.569
MA0080.25.41382e-6
MA0081.10.051
MA0083.10.0411
MA0084.10.216
MA0087.10.105
MA0088.10.18
MA0090.10.685
MA0091.10.443
MA0092.10.232
MA0093.10.357
MA0099.27.83788e-20
MA0100.10.668
MA0101.10.00217
MA0102.20.381
MA0103.10.0925
MA0104.20.273
MA0105.13.08246e-5
MA0106.10.0124
MA0107.10.00163
MA0108.20.453
MA0111.10.598
MA0112.25.35386e-4
MA0113.10.963
MA0114.10.0097
MA0115.10.633
MA0116.10.0023
MA0117.10.792
MA0119.10.163
MA0122.10.635
MA0124.10.75
MA0125.10.214
MA0131.10.948
MA0135.10.00612
MA0136.11.7919e-9
MA0137.20.062
MA0138.20.398
MA0139.10.566
MA0140.10.00534
MA0141.10.0062
MA0142.10.291
MA0143.10.0924
MA0144.10.89
MA0145.10.43
MA0146.10.0296
MA0147.10.125
MA0148.10.487
MA0149.10.0157
MA0150.11.18199e-4
MA0152.10.279
MA0153.10.584
MA0154.10.0346
MA0155.10.652
MA0156.12.73633e-6
MA0157.10.826
MA0159.10.0119
MA0160.10.0291
MA0162.10.161
MA0163.19.18354e-9
MA0164.10.542
MA0258.10.0121
MA0259.10.502



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: CNhs12315

Novel motifP-value
10.038
100.0378
1000.358
1010.705
1020.96
1030.0502
1040.0961
1050.235
1060.0299
1070.153
1080.789
1090.00392
110.00798
1100.0525
1110.0547
1120.391
1130.31
1140.0672
1150.897
1160.21
1170.0108
1180.152
1190.23
120.621
1200.132
1210.718
1220.989
1230.834
1240.283
1250.361
1260.0673
1270.406
1280.211
1290.519
130.00584
1300.417
1310.0232
1320.427
1330.165
1340.567
1350.272
1360.00496
1370.829
1380.729
1390.0878
140.97
1400.569
1410.478
1420.963
1430.00847
1440.954
1450.212
1460.694
1470.788
1480.188
1490.107
150.0452
1500.126
1510.723
1520.126
1530.948
1540.547
1550.477
1560.256
1570.35
1580.248
1590.00729
160.0429
1600.204
1610.2
1620.785
1630.737
1640.0132
1650.215
1660.722
1670.632
1680.72
1690.0156
170.0825
180.0353
190.336
20.944
200.144
210.0304
220.311
230.563
240.117
250.565
267.91909e-4
270.637
280.822
290.00595
30.05
300.625
310.911
320.0104
330.084
340.785
350.442
360.169
370.0506
380.437
390.418
40.632
400.0783
410.178
420.227
430.124
440.112
450.821
460.0252
470.0389
480.0462
490.246
50.63
500.498
510.282
520.787
530.668
540.407
550.772
560.585
570.261
580.347
590.0922
60.937
600.117
610.136
620.166
630.24
640.143
650.287
660.0918
670.328
680.116
690.202
70.119
700.022
710.008
720.46
730.0472
740.94
750.0173
760.176
770.297
784.63738e-4
790.266
80.0514
800.827
810.499
820.637
830.0806
840.467
850.318
860.175
870.00105
880.74
890.158
90.58
900.057
910.552
920.514
930.756
940.101
950.0257
960.981
970.769
980.152
990.683



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: CNhs12315


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)

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0001896 (medulla oblongata)
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)
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)
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)
0002298 (brainstem)
0002028 (hindbrain)
0005290 (myelencephalon)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010038 (human medulla oblongata - adult 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

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