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|library_id=CNhs11935
|library_id=CNhs11935
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|library_id_phase_based=2:CNhs11935
|name="lymphoma, malignant, hairy B-cell cell line:MLMA"
|name=lymphoma, malignant, hairy B-cell cell line:MLMA
|namespace=FANTOM5
|namespace=FANTOM5
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Line 77: Line 77:
|sample_description=
|sample_description=
|sample_dev_stage=
|sample_dev_stage=
|sample_disease="lymphoma, malignant, hairy B-cell"
|sample_disease=lymphoma, malignant, hairy B-cell
|sample_donor(cell lot)=
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_ethnicity=J

Revision as of 18:03, 27 November 2014


Name:lymphoma, malignant, hairy B-cell cell line:MLMA
Species:Human (Homo sapiens)
Library ID:CNhs11935
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexfemale
age32
cell typeb cell
cell lineMLMA
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  SAMD00005415
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11935 CAGE DRX007925 DRR008797
Accession ID Hg19

Library idBAMCTSS
CNhs11935 DRZ000222 DRZ001607
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-penis0.0678
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11935

Jaspar motifP-value
MA0002.20.0646
MA0003.10.466
MA0004.10.182
MA0006.10.373
MA0007.10.598
MA0009.10.88
MA0014.10.88
MA0017.10.462
MA0018.20.175
MA0019.10.579
MA0024.18.36414e-11
MA0025.10.644
MA0027.10.138
MA0028.11.47263e-6
MA0029.10.652
MA0030.10.346
MA0031.10.958
MA0035.20.255
MA0038.10.00552
MA0039.20.607
MA0040.10.126
MA0041.10.229
MA0042.10.467
MA0043.10.369
MA0046.10.193
MA0047.20.352
MA0048.10.869
MA0050.10.0186
MA0051.10.0781
MA0052.10.0677
MA0055.10.396
MA0057.10.736
MA0058.10.225
MA0059.10.0271
MA0060.11.2369e-10
MA0061.12.27076e-4
MA0062.23.44524e-11
MA0065.20.105
MA0066.10.467
MA0067.10.625
MA0068.10.207
MA0069.10.812
MA0070.10.45
MA0071.10.88
MA0072.10.357
MA0073.10.975
MA0074.10.474
MA0076.11.88951e-10
MA0077.10.685
MA0078.10.306
MA0079.20.332
MA0080.28.52803e-5
MA0081.10.00686
MA0083.13.63714e-4
MA0084.10.322
MA0087.10.356
MA0088.10.0164
MA0090.15.30148e-6
MA0091.10.864
MA0092.10.376
MA0093.10.235
MA0099.22.66734e-10
MA0100.10.0539
MA0101.10.00312
MA0102.20.301
MA0103.10.00109
MA0104.20.00237
MA0105.14.89939e-5
MA0106.10.751
MA0107.10.0041
MA0108.21.13819e-10
MA0111.10.148
MA0112.20.971
MA0113.10.114
MA0114.10.143
MA0115.10.202
MA0116.10.00161
MA0117.10.897
MA0119.10.252
MA0122.10.922
MA0124.10.909
MA0125.10.374
MA0131.10.075
MA0135.10.0427
MA0136.14.0761e-9
MA0137.20.1
MA0138.20.699
MA0139.10.346
MA0140.10.0725
MA0141.10.736
MA0142.10.0123
MA0143.10.243
MA0144.10.00731
MA0145.10.271
MA0146.10.603
MA0147.17.96415e-4
MA0148.10.569
MA0149.10.0792
MA0150.10.0145
MA0152.10.345
MA0153.10.0461
MA0154.10.0768
MA0155.10.24
MA0156.15.1369e-6
MA0157.10.27
MA0159.10.583
MA0160.10.484
MA0162.10.509
MA0163.11.03325e-5
MA0164.10.983
MA0258.10.642
MA0259.10.0837



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: CNhs11935

Novel motifP-value
10.139
100.0253
1000.607
1010.244
1020.435
1030.563
1040.486
1050.746
1060.811
1070.745
1080.794
1090.244
110.269
1100.511
1110.111
1120.717
1130.617
1140.939
1150.749
1160.553
1170.014
1180.475
1190.364
120.697
1200.444
1210.39
1220.326
1230.0431
1240.173
1250.224
1260.509
1270.799
1280.525
1290.543
130.158
1300.494
1310.169
1320.0975
1330.958
1340.713
1350.943
1360.0409
1370.458
1380.979
1390.399
140.787
1400.692
1410.304
1420.562
1430.383
1440.212
1450.103
1460.453
1470.0694
1480.134
1490.346
150.153
1500.781
1510.636
1520.0709
1530.712
1540.901
1550.0118
1560.655
1570.134
1580.807
1590.243
160.999
1600.78
1610.314
1620.55
1630.202
1640.502
1650.507
1660.21
1670.172
1680.887
1690.341
170.761
180.926
190.357
20.32
200.454
210.354
220.493
230.07
240.789
250.0219
260.157
270.78
280.496
290.0193
30.271
300.117
310.617
320.209
330.946
340.342
350.317
360.0668
370.638
380.842
390.439
40.0311
400.16
410.666
420.135
430.636
440.242
450.423
460.221
470.0757
480.198
490.135
50.555
500.897
510.929
520.285
530.408
540.564
550.507
560.816
570.303
580.169
590.896
60.866
600.715
610.0923
620.165
630.814
640.51
650.322
660.0012
670.974
680.0573
690.355
70.107
700.354
710.0344
720.875
730.675
740.913
750.00283
760.332
770.0656
780.115
790.556
80.509
800.89
810.0873
820.433
830.517
840.402
850.0717
860.426
870.0415
880.49
890.45
90.556
906.41817e-4
910.437
920.658
930.707
940.496
950.246
960.656
970.163
980.591
990.385



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: CNhs11935


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)

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)

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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