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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423,UBERON:0007195
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423,UBERON:0007195
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0103296
|fonse_cell_line=FF:0103296
|fonse_cell_line_closure=FF:0103296
|fonse_cell_line_closure=FF:0103296

Revision as of 17:01, 29 March 2012


Name:bone marrow stromal cell line:StromaNKtert
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexunknown
ageNA
cell typestromal cell
cell lineStromaNKtert
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

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
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-penis-0.115
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.328
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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 no result for this sample


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: CNhs11931

Jaspar motifP-value
MA0002.20.224
MA0003.10.167
MA0004.10.306
MA0006.10.593
MA0007.10.234
MA0009.10.676
MA0014.10.971
MA0017.10.86
MA0018.20.0271
MA0019.10.432
MA0024.10.804
MA0025.10.0127
MA0027.10.497
MA0028.16.17158e-6
MA0029.10.142
MA0030.10.496
MA0031.10.812
MA0035.20.127
MA0038.10.922
MA0039.20.031
MA0040.10.617
MA0041.10.271
MA0042.10.0555
MA0043.10.00426
MA0046.10.766
MA0047.20.386
MA0048.10.442
MA0050.10.8
MA0051.10.798
MA0052.10.447
MA0055.10.533
MA0057.10.892
MA0058.10.209
MA0059.10.524
MA0060.10.503
MA0061.10.531
MA0062.22.58542e-12
MA0065.20.503
MA0066.10.296
MA0067.10.185
MA0068.10.849
MA0069.10.534
MA0070.10.369
MA0071.10.696
MA0072.10.665
MA0073.10.887
MA0074.10.208
MA0076.13.64633e-7
MA0077.10.414
MA0078.10.538
MA0079.20.445
MA0080.27.65732e-4
MA0081.10.252
MA0083.19.12456e-5
MA0084.10.0858
MA0087.10.522
MA0088.10.714
MA0090.12.11278e-9
MA0091.10.453
MA0092.10.0678
MA0093.10.255
MA0099.25.30188e-9
MA0100.10.976
MA0101.10.863
MA0102.20.309
MA0103.10.00659
MA0104.20.0536
MA0105.10.62
MA0106.10.368
MA0107.10.811
MA0108.20.0876
MA0111.10.715
MA0112.20.153
MA0113.10.00536
MA0114.10.667
MA0115.10.972
MA0116.10.804
MA0117.10.493
MA0119.10.00145
MA0122.10.897
MA0124.10.601
MA0125.10.911
MA0131.10.258
MA0135.10.243
MA0136.10.00462
MA0137.20.175
MA0138.20.24
MA0139.10.371
MA0140.10.418
MA0141.10.697
MA0142.10.426
MA0143.10.598
MA0144.10.977
MA0145.10.0261
MA0146.10.115
MA0147.10.21
MA0148.10.0512
MA0149.10.559
MA0150.10.0162
MA0152.10.0408
MA0153.10.851
MA0154.10.307
MA0155.10.374
MA0156.10.0227
MA0157.10.217
MA0159.10.957
MA0160.10.978
MA0162.10.611
MA0163.10.666
MA0164.10.714
MA0258.10.333
MA0259.10.293



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: CNhs11931

Novel motifP-value
10.0481
100.387
1000.206
1010.839
1020.0272
1030.382
1040.416
1050.308
1060.322
1070.0028
1080.957
1090.927
110.482
1100.871
1110.193
1120.557
1130.327
1140.567
1150.163
1160.692
1170.479
1180.104
1190.325
120.797
1200.809
1210.963
1220.668
1230.623
1240.724
1250.764
1260.83
1270.634
1280.585
1290.186
130.915
1300.0635
1310.622
1320.306
1330.998
1340.192
1350.743
1360.132
1370.521
1380.845
1390.337
140.227
1400.135
1410.429
1420.648
1430.248
1440.602
1450.0669
1460.189
1470.582
1480.234
1490.484
150.213
1500.11
1510.491
1520.306
1530.401
1540.849
1550.116
1560.608
1570.221
1580.568
1590.644
160.509
1600.938
1610.641
1620.816
1630.966
1640.0822
1650.86
1660.436
1670.901
1680.415
1690.434
170.163
180.262
190.111
20.738
200.929
210.403
220.431
230.0101
240.44
250.528
260.286
270.887
280.723
290.197
30.654
300.989
310.508
320.0604
330.764
340.596
350.813
360.976
370.799
380.464
390.499
40.883
400.352
410.45
420.495
430.219
440.207
450.523
460.149
470.87
480.995
490.139
50.257
500.665
510.68
520.832
530.926
540.124
550.0399
560.619
570.108
580.76
590.164
60.94
600.643
610.578
620.45
630.451
640.63
650.201
660.117
670.396
680.812
690.979
70.865
700.627
710.539
720.554
730.738
740.124
750.207
760.166
770.182
780.727
790.968
80.175
800.137
810.362
820.642
830.088
840.362
850.342
860.791
870.902
880.618
890.866
90.649
900.369
910.663
920.379
930.453
940.0727
950.0537
960.0771
970.0439
980.697
990.182



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: CNhs11931


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

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)
0007195 (stroma of bone marrow)

FF: FANTOM5
NA

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
NA

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