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Revision as of 18:12, 27 November 2014


Name:hereditary spherocytic anemia cell line:WIL2-NS
Species:Human (Homo sapiens)
Library ID:CNhs11891
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
ageunknown
cell typeb cell
cell lineWIL2-NS
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00005140
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11891 CAGE DRX007909 DRR008781
Accession ID Hg19

Library idBAMCTSS
CNhs11891 DRZ000206 DRZ001591
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-penis0.131
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-lymphoma0.622
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11891

Jaspar motifP-value
MA0002.20.074
MA0003.10.754
MA0004.10.034
MA0006.10.199
MA0007.10.277
MA0009.10.645
MA0014.10.593
MA0017.10.0866
MA0018.20.809
MA0019.10.148
MA0024.18.30168e-10
MA0025.10.567
MA0027.10.334
MA0028.13.862e-7
MA0029.10.416
MA0030.10.00157
MA0031.10.0438
MA0035.20.272
MA0038.10.0327
MA0039.20.373
MA0040.10.00984
MA0041.10.0919
MA0042.10.291
MA0043.10.426
MA0046.10.459
MA0047.20.299
MA0048.10.169
MA0050.11.40548e-7
MA0051.14.25855e-5
MA0052.10.764
MA0055.10.0123
MA0057.10.927
MA0058.10.0198
MA0059.11.59415e-4
MA0060.11.59835e-14
MA0061.10.0022
MA0062.22.33702e-11
MA0065.20.0186
MA0066.10.779
MA0067.10.697
MA0068.10.151
MA0069.10.282
MA0070.10.673
MA0071.10.611
MA0072.10.0602
MA0073.10.685
MA0074.10.557
MA0076.14.34502e-10
MA0077.10.377
MA0078.10.273
MA0079.20.119
MA0080.20.00179
MA0081.10.0349
MA0083.10.0323
MA0084.10.093
MA0087.10.0404
MA0088.15.37063e-4
MA0090.18.64946e-6
MA0091.10.567
MA0092.10.88
MA0093.10.0228
MA0099.20.00748
MA0100.10.0166
MA0101.10.0049
MA0102.20.154
MA0103.10.151
MA0104.26.7735e-5
MA0105.17.21916e-5
MA0106.10.344
MA0107.10.00649
MA0108.26.5201e-8
MA0111.10.498
MA0112.20.359
MA0113.10.756
MA0114.10.0123
MA0115.10.124
MA0116.12.69588e-4
MA0117.10.808
MA0119.10.799
MA0122.10.473
MA0124.10.603
MA0125.10.234
MA0131.10.0863
MA0135.10.602
MA0136.12.8387e-8
MA0137.20.238
MA0138.20.42
MA0139.10.0898
MA0140.10.0422
MA0141.10.0891
MA0142.10.0282
MA0143.10.188
MA0144.10.367
MA0145.10.452
MA0146.10.712
MA0147.12.48917e-5
MA0148.10.283
MA0149.10.154
MA0150.10.817
MA0152.10.286
MA0153.10.0528
MA0154.10.032
MA0155.10.659
MA0156.12.64166e-10
MA0157.10.818
MA0159.10.196
MA0160.10.496
MA0162.10.78
MA0163.12.00722e-10
MA0164.10.793
MA0258.10.409
MA0259.10.038



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: CNhs11891

Novel motifP-value
10.00495
100.0165
1000.348
1010.0627
1020.661
1030.139
1040.359
1050.668
1060.341
1070.128
1080.883
1090.027
110.0724
1100.0967
1110.117
1120.923
1130.625
1140.505
1150.825
1160.648
1170.00884
1180.149
1190.185
120.993
1200.296
1210.674
1220.504
1230.0085
1240.107
1250.391
1260.315
1270.104
1280.275
1290.502
130.0439
1300.283
1310.378
1320.104
1330.531
1340.513
1350.559
1360.182
1370.819
1380.513
1390.516
140.953
1400.698
1410.0284
1420.989
1430.0978
1440.559
1450.258
1460.894
1470.967
1480.0981
1490.306
150.0352
1500.998
1510.616
1520.0388
1530.998
1540.641
1550.322
1560.796
1570.146
1580.968
1590.248
160.961
1600.224
1610.0553
1620.772
1630.439
1640.266
1650.868
1660.482
1670.0728
1680.537
1690.937
170.981
180.185
190.783
20.596
200.378
210.128
220.894
230.0328
240.308
250.213
260.0276
270.688
280.302
290.00882
30.111
300.156
310.969
320.395
330.304
340.352
350.061
360.0392
370.307
380.559
390.327
40.137
400.264
410.754
420.0485
430.592
440.0901
450.431
460.179
470.0173
480.112
490.272
50.976
500.744
510.742
520.083
530.611
540.774
550.745
560.696
570.226
580.314
590.777
60.774
600.671
610.057
620.303
630.813
640.176
650.764
660.00604
670.275
680.0269
690.704
70.0972
700.54
710.0178
720.564
730.901
740.792
750.00307
760.474
770.749
780.272
790.0537
80.068
800.458
810.227
820.658
830.149
840.917
850.29
860.251
870.182
880.705
890.636
90.578
900.124
910.0314
920.683
930.332
940.243
950.0137
960.554
970.142
980.311
990.817



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: CNhs11891


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000945 (lymphocyte of B lineage)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
0060058 (lymphoma)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1287 (cardiovascular system disease)
7 (disease of anatomical entity)
74 (hematopoietic system disease)
2355 (anemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100104 (lymphoma cell line sample)
0101518 (B-lymphoma cell line sample)
0101524 (WIL2-NS 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)
CL:0000051 (common lymphoid progenitor)

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