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FF:10840-111E3: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101035,FF:0101522
|fonse_cell_line=FF:0101035,FF:0101522
|fonse_cell_line_closure=FF:0101035,FF:0101522
|fonse_cell_line_closure=FF:0101035,FF:0101522

Revision as of 17:24, 29 March 2012


Name:plasma cell leukemia cell line:ARH-77
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexfemale
age33
cell typeplasma cell
cell lineARH-77
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
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-penis0.101
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0182
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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 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: CNhs12807

Jaspar motifP-value
MA0002.20.0139
MA0003.10.522
MA0004.10.0129
MA0006.10.172
MA0007.10.702
MA0009.10.612
MA0014.10.937
MA0017.10.486
MA0018.20.593
MA0019.10.967
MA0024.11.50395e-7
MA0025.10.502
MA0027.10.816
MA0028.12.53444e-5
MA0029.10.327
MA0030.10.106
MA0031.10.603
MA0035.20.113
MA0038.10.133
MA0039.20.964
MA0040.10.11
MA0041.10.227
MA0042.10.466
MA0043.10.949
MA0046.10.252
MA0047.20.852
MA0048.10.936
MA0050.11.39552e-19
MA0051.11.29241e-14
MA0052.10.401
MA0055.10.157
MA0057.10.767
MA0058.10.00846
MA0059.12.43636e-4
MA0060.14.98294e-17
MA0061.13.37274e-9
MA0062.22.02209e-8
MA0065.20.0671
MA0066.10.706
MA0067.10.478
MA0068.10.257
MA0069.10.927
MA0070.10.762
MA0071.10.834
MA0072.10.12
MA0073.10.595
MA0074.10.644
MA0076.15.13093e-8
MA0077.10.446
MA0078.10.107
MA0079.20.32
MA0080.22.99287e-5
MA0081.10.0209
MA0083.10.416
MA0084.10.105
MA0087.10.0903
MA0088.10.0274
MA0090.11.91167e-5
MA0091.10.856
MA0092.10.521
MA0093.10.0106
MA0099.20.00131
MA0100.10.0561
MA0101.11.34007e-7
MA0102.20.354
MA0103.10.0204
MA0104.21.04975e-4
MA0105.14.25612e-8
MA0106.10.903
MA0107.13.70235e-8
MA0108.20.101
MA0111.10.522
MA0112.20.927
MA0113.10.307
MA0114.10.197
MA0115.10.272
MA0116.10.00101
MA0117.10.724
MA0119.10.421
MA0122.10.387
MA0124.10.384
MA0125.10.55
MA0131.10.136
MA0135.10.529
MA0136.13.89651e-8
MA0137.20.425
MA0138.20.973
MA0139.10.231
MA0140.10.00625
MA0141.10.431
MA0142.10.194
MA0143.10.287
MA0144.10.0755
MA0145.10.128
MA0146.10.727
MA0147.14.32092e-5
MA0148.10.268
MA0149.10.238
MA0150.10.546
MA0152.10.172
MA0153.10.0943
MA0154.10.012
MA0155.10.556
MA0156.11.7092e-9
MA0157.10.924
MA0159.10.218
MA0160.10.375
MA0162.10.492
MA0163.12.8517e-8
MA0164.10.262
MA0258.10.514
MA0259.10.0129



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: CNhs12807

Novel motifP-value
10.143
100.0245
1000.216
1010.457
1020.473
1030.332
1040.579
1050.479
1060.801
1070.313
1080.938
1090.0963
110.532
1100.613
1110.044
1120.888
1130.858
1140.726
1150.5
1160.723
1170.0313
1180.56
1190.395
120.674
1200.871
1210.195
1220.344
1230.202
1240.019
1250.559
1260.132
1270.561
1280.145
1290.294
130.0447
1300.257
1310.52
1320.121
1330.258
1340.558
1350.642
1360.16
1370.58
1380.558
1390.846
140.828
1400.203
1410.00515
1420.791
1430.0276
1440.458
1450.758
1460.931
1470.263
1480.172
1490.389
150.0592
1500.859
1510.161
1520.0571
1530.795
1540.617
1550.108
1560.764
1570.214
1580.412
1590.332
160.356
1600.418
1610.0374
1620.558
1630.948
1640.958
1650.912
1660.253
1670.134
1680.719
1690.216
170.913
180.419
190.496
20.133
200.106
210.44
220.499
230.207
240.0491
250.0622
260.152
270.92
280.561
290.00351
30.446
300.0761
310.794
320.189
330.3
340.519
350.231
360.0404
370.723
380.446
390.247
40.0381
400.114
410.492
420.263
430.455
440.213
450.261
460.454
470.128
480.273
490.159
50.637
500.741
510.697
520.186
530.777
540.283
550.184
560.941
570.798
580.07
590.657
60.988
600.933
610.229
620.131
630.59
640.773
650.691
664.18633e-5
670.491
680.229
690.83
70.128
700.789
710.0308
720.186
730.56
740.961
750.0185
760.153
770.0221
780.162
790.689
80.556
800.257
810.264
820.365
830.096
840.696
850.308
860.368
870.088
880.697
890.354
90.425
900.309
910.505
920.711
930.419
940.928
950.00716
960.8
970.179
980.832
990.0575



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: CNhs12807


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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000236 (B cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000785 (mature B cell)
0000786 (plasma cell)
0000816 (immature B cell)
0000817 (precursor B cell)
0000818 (transitional stage B cell)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000946 (antibody secreting cell)
0000954 (small pre-B-II cell)
0000955 (pre-B-II cell)
0000980 (plasmablast)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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