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FF:12214-129D9: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:13, 29 March 2012


Name:CD19+ B Cells (pluriselect), donor090612, donation3
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
sexNA
ageNA
cell typeb cell
cell lineNA
companyNA
collaborationMatched_genome_OSC(contact:Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-0.105
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-lymphoma-0.201
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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: CNhs12188

Jaspar motifP-value
MA0002.23.6557e-6
MA0003.10.53
MA0004.10.363
MA0006.10.313
MA0007.10.677
MA0009.10.934
MA0014.10.426
MA0017.10.0369
MA0018.20.383
MA0019.10.53
MA0024.10.948
MA0025.10.51
MA0027.10.501
MA0028.12.00207e-5
MA0029.10.894
MA0030.10.0419
MA0031.10.0898
MA0035.20.268
MA0038.10.621
MA0039.20.557
MA0040.10.871
MA0041.10.0995
MA0042.10.692
MA0043.10.681
MA0046.10.849
MA0047.20.385
MA0048.10.57
MA0050.13.8851e-10
MA0051.15.41444e-5
MA0052.10.194
MA0055.10.326
MA0057.10.826
MA0058.10.214
MA0059.10.201
MA0060.10.903
MA0061.16.24792e-5
MA0062.24.08004e-15
MA0065.20.0328
MA0066.10.34
MA0067.10.474
MA0068.10.38
MA0069.10.469
MA0070.10.383
MA0071.10.676
MA0072.10.729
MA0073.10.652
MA0074.10.734
MA0076.12.68336e-8
MA0077.10.279
MA0078.10.766
MA0079.20.489
MA0080.21.39282e-11
MA0081.14.95923e-4
MA0083.10.143
MA0084.10.366
MA0087.10.349
MA0088.10.101
MA0090.11.77186e-4
MA0091.10.595
MA0092.10.668
MA0093.10.438
MA0099.20.00246
MA0100.10.259
MA0101.10.00626
MA0102.20.534
MA0103.10.00811
MA0104.20.089
MA0105.11.2206e-7
MA0106.10.342
MA0107.10.00308
MA0108.23.37733e-7
MA0111.10.395
MA0112.20.0429
MA0113.10.828
MA0114.10.103
MA0115.10.382
MA0116.12.80284e-5
MA0117.10.473
MA0119.10.447
MA0122.10.257
MA0124.10.878
MA0125.10.649
MA0131.10.0838
MA0135.10.0489
MA0136.11.84816e-17
MA0137.20.606
MA0138.20.61
MA0139.10.203
MA0140.10.0786
MA0141.10.842
MA0142.10.125
MA0143.10.965
MA0144.10.939
MA0145.10.742
MA0146.10.37
MA0147.10.0795
MA0148.10.812
MA0149.10.0853
MA0150.10.602
MA0152.10.413
MA0153.10.125
MA0154.15.93054e-4
MA0155.10.879
MA0156.16.902e-15
MA0157.10.0725
MA0159.10.0293
MA0160.10.524
MA0162.10.893
MA0163.19.1666e-9
MA0164.10.95
MA0258.10.155
MA0259.10.368



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: CNhs12188

Novel motifP-value
10.121
100.0398
1000.609
1010.5
1020.993
1030.125
1040.177
1050.323
1060.652
1070.227
1080.229
1090.111
110.21
1100.16
1110.288
1120.252
1130.0347
1140.531
1150.867
1160.71
1170.00148
1180.171
1190.721
120.998
1200.546
1210.424
1220.311
1230.236
1240.114
1250.37
1260.411
1270.598
1280.472
1290.822
130.428
1300.565
1310.58
1320.351
1330.0118
1340.772
1350.63
1360.601
1370.129
1380.614
1390.158
140.369
1400.973
1410.633
1420.655
1430.0282
1440.714
1450.483
1460.124
1470.105
1480.108
1490.445
150.128
1500.739
1510.728
1520.484
1530.697
1540.852
1550.00441
1560.293
1570.26
1580.158
1590.137
160.948
1600.352
1610.11
1620.849
1630.334
1640.435
1650.203
1660.802
1670.144
1680.127
1690.562
170.722
180.451
190.675
20.81
200.593
210.87
220.782
230.695
240.443
250.0152
260.192
270.205
280.477
290.0748
30.0689
300.38
310.768
320.33
330.467
340.892
350.139
360.0226
370.159
380.594
390.481
40.582
400.185
410.138
420.114
430.162
440.484
450.945
460.188
470.124
480.196
490.12
50.406
500.855
510.486
520.442
530.478
540.784
550.11
560.678
570.504
580.0218
590.32
60.77
600.444
610.0225
620.0188
630.748
640.388
650.865
660.848
670.638
680.278
690.737
70.0718
700.189
710.0381
720.0201
730.58
740.258
750.0141
760.0754
770.655
780.15
790.373
80.659
800.00334
810.233
820.113
830.839
840.336
850.972
860.0931
870.222
880.903
890.648
90.393
900.0289
910.637
920.755
930.891
940.0578
950.0103
960.438
970.495
980.211
990.0455



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: CNhs12188


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)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
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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