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|DRA_sample_Accession=CAGE@SAMD00005930
|DRA_sample_Accession=CAGE@SAMD00005930
|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005930
|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005930
|accession_numbers=CAGE;DRX007902;DRR008774;DRZ000199;DRZ001584
|accession_numbers=CAGE;DRX007902;DRR008774;DRZ000199;DRZ001584;DRZ011549;DRZ012934
|accession_numbers_RNASeq=RNA-Seq;DRX057136;DRR062895;DRZ007971
|accession_numbers_RNASeq=RNA-Seq;DRX057136;DRR062895;DRZ007971
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
Line 64: Line 64:
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
|refex=http://refex.dbcls.jp/genelist.php?lang
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Revision as of 19:40, 10 August 2017

Name:hairy cell leukemia cell line:Mo
Species:Human (Homo sapiens)
Library ID:CNhs11843
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
ageNA
cell typet cell
cell lineMo
companyATCC
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  SAMD00005930
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11843 CAGE DRX007902 DRR008774
Accession ID Hg19

Library idBAMCTSS
CNhs11843 DRZ000199 DRZ001584
Accession ID Hg38

Library idBAMCTSS
CNhs11843 DRZ011549 DRZ012934
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
RNA-Seq  SAMD00005930
Library accession numbers

Library idMethodExp. accession idRun accession id
RDhi10079 RNA-Seq DRX057136 DRR062895
Accession ID Hg19

Library idBAMCTSS
RDhi10079 DRZ007971


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-penis0.476
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-lymphoma0.438
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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-parotid1.17



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: CNhs11843

Jaspar motifP-value
MA0002.20.00865
MA0003.10.608
MA0004.10.191
MA0006.10.218
MA0007.10.987
MA0009.10.82
MA0014.10.729
MA0017.10.2
MA0018.22.03624e-4
MA0019.10.268
MA0024.12.38578e-4
MA0025.10.179
MA0027.10.15
MA0028.10.00847
MA0029.10.958
MA0030.10.00134
MA0031.10.0141
MA0035.20.00957
MA0038.10.435
MA0039.20.722
MA0040.10.0122
MA0041.10.0317
MA0042.10.0938
MA0043.10.535
MA0046.10.17
MA0047.20.306
MA0048.10.22
MA0050.10.512
MA0051.10.843
MA0052.10.154
MA0055.10.00536
MA0057.10.951
MA0058.10.218
MA0059.10.0514
MA0060.12.89195e-4
MA0061.11.36793e-9
MA0062.23.65188e-5
MA0065.20.0148
MA0066.10.911
MA0067.10.147
MA0068.10.0651
MA0069.10.438
MA0070.10.901
MA0071.10.37
MA0072.10.33
MA0073.10.722
MA0074.10.817
MA0076.10.00677
MA0077.10.616
MA0078.10.846
MA0079.20.315
MA0080.20.0018
MA0081.10.901
MA0083.10.715
MA0084.10.117
MA0087.10.104
MA0088.10.0294
MA0090.14.57039e-5
MA0091.10.197
MA0092.10.951
MA0093.10.167
MA0099.20.0172
MA0100.10.522
MA0101.16.75242e-9
MA0102.20.0288
MA0103.10.329
MA0104.20.00521
MA0105.12.65572e-9
MA0106.10.136
MA0107.13.13391e-9
MA0108.22.61233e-4
MA0111.10.513
MA0112.20.109
MA0113.10.89
MA0114.10.0438
MA0115.10.258
MA0116.11.52088e-5
MA0117.10.315
MA0119.10.848
MA0122.10.872
MA0124.10.499
MA0125.10.963
MA0131.10.152
MA0135.10.128
MA0136.14.24382e-4
MA0137.20.0304
MA0138.20.483
MA0139.10.0884
MA0140.10.0995
MA0141.10.0395
MA0142.10.847
MA0143.10.508
MA0144.10.0585
MA0145.10.762
MA0146.10.142
MA0147.10.00219
MA0148.10.225
MA0149.10.369
MA0150.10.736
MA0152.10.102
MA0153.14.84111e-4
MA0154.10.0278
MA0155.10.936
MA0156.10.00395
MA0157.10.132
MA0159.10.202
MA0160.10.051
MA0162.10.617
MA0163.14.85318e-12
MA0164.10.67
MA0258.10.0719
MA0259.10.0474



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: CNhs11843

Novel motifP-value
10.0136
100.019
1000.214
1010.811
1020.307
1030.48
1040.685
1050.796
1060.88
1070.361
1080.997
1090.0477
110.0827
1100.16
1110.0344
1120.172
1130.702
1140.11
1150.964
1160.244
1170.0329
1180.172
1190.105
120.902
1200.834
1210.929
1221
1232.13271e-4
1240.257
1250.298
1260.995
1270.415
1280.736
1290.299
130.0177
1300.768
1310.812
1320.565
1330.934
1340.702
1350.445
1360.119
1370.638
1380.877
1390.182
140.915
1400.115
1410.72
1420.771
1430.0711
1440.649
1450.509
1460.793
1470.0842
1480.129
1490.0654
150.205
1500.904
1510.884
1520.253
1530.945
1540.711
1550.0287
1560.384
1570.97
1580.256
1590.102
160.744
1600.252
1610.826
1620.921
1630.274
1640.429
1650.488
1660.0493
1670.0483
1680.543
1690.52
170.544
180.172
190.719
20.323
200.117
210.113
220.867
230.494
240.15
250.0998
260.141
270.931
280.905
290.0188
30.141
300.0796
310.68
320.85
330.555
340.611
350.162
360.0405
370.321
380.81
390.488
40.204
400.192
410.652
420.171
430.358
440.0561
450.339
460.13
470.11
480.218
490.122
50.912
500.74
510.494
520.438
530.586
540.81
550.0539
560.864
570.137
580.0992
590.778
60.781
600.812
610.149
620.0698
630.656
640.168
650.945
660.0437
670.207
680.153
690.565
70.22
700.305
710.0351
720.82
730.704
740.822
750.0396
760.487
770.465
780.266
790.869
80.348
800.36
810.0803
820.467
830.0478
840.115
850.461
860.388
870.397
880.827
890.987
90.641
900.242
910.532
920.874
930.975
940.229
950.043
960.4
970.0493
980.288
990.135



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: CNhs11843


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)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000084 (T cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100737 (leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0103681 (hairy cell leukemia cell line sample)
0101014 (Mo-T 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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