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FF:12199-129C3: 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), donor090309, 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-0.0728
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-0.221
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 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: CNhs12181

Jaspar motifP-value
MA0002.28.74166e-6
MA0003.10.567
MA0004.10.3
MA0006.10.379
MA0007.10.783
MA0009.10.798
MA0014.10.881
MA0017.10.091
MA0018.20.994
MA0019.10.705
MA0024.10.851
MA0025.10.645
MA0027.10.81
MA0028.13.94867e-5
MA0029.10.727
MA0030.10.0225
MA0031.10.0503
MA0035.20.443
MA0038.10.111
MA0039.20.758
MA0040.10.947
MA0041.10.16
MA0042.10.805
MA0043.10.806
MA0046.10.976
MA0047.20.165
MA0048.10.451
MA0050.19.38537e-12
MA0051.14.97101e-5
MA0052.10.243
MA0055.10.76
MA0057.10.705
MA0058.10.201
MA0059.10.272
MA0060.10.391
MA0061.11.41794e-4
MA0062.23.32705e-14
MA0065.20.0276
MA0066.10.592
MA0067.10.608
MA0068.10.369
MA0069.10.553
MA0070.10.705
MA0071.10.741
MA0072.10.535
MA0073.10.821
MA0074.10.704
MA0076.16.50952e-8
MA0077.10.416
MA0078.10.744
MA0079.20.31
MA0080.24.29764e-11
MA0081.12.06019e-4
MA0083.10.0609
MA0084.10.335
MA0087.10.341
MA0088.10.119
MA0090.14.34032e-4
MA0091.10.884
MA0092.10.82
MA0093.10.343
MA0099.22.25179e-4
MA0100.10.155
MA0101.10.0229
MA0102.20.301
MA0103.10.0105
MA0104.20.0858
MA0105.17.27834e-7
MA0106.10.464
MA0107.10.0129
MA0108.21.23173e-8
MA0111.10.356
MA0112.20.0236
MA0113.10.892
MA0114.10.0963
MA0115.10.341
MA0116.12.29382e-5
MA0117.10.75
MA0119.10.52
MA0122.10.656
MA0124.10.647
MA0125.10.833
MA0131.10.0781
MA0135.10.0278
MA0136.13.9392e-17
MA0137.20.977
MA0138.20.631
MA0139.10.197
MA0140.10.171
MA0141.10.917
MA0142.10.145
MA0143.10.525
MA0144.10.581
MA0145.10.683
MA0146.10.347
MA0147.10.0934
MA0148.10.484
MA0149.10.097
MA0150.10.385
MA0152.10.308
MA0153.10.0433
MA0154.14.95108e-4
MA0155.10.709
MA0156.11.83974e-13
MA0157.10.0859
MA0159.10.0401
MA0160.10.454
MA0162.10.988
MA0163.18.63212e-9
MA0164.10.857
MA0258.10.121
MA0259.10.394



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: CNhs12181

Novel motifP-value
10.0921
100.0366
1000.6
1010.278
1020.93
1030.0434
1040.111
1050.322
1060.834
1070.384
1080.32
1090.0647
110.0808
1100.149
1110.114
1120.34
1130.0289
1140.415
1150.851
1160.779
1170.00232
1180.109
1190.497
120.853
1200.572
1210.458
1220.343
1230.0251
1240.139
1250.34
1260.252
1270.643
1280.428
1290.556
130.542
1300.542
1310.846
1320.375
1330.00109
1340.606
1350.512
1360.499
1370.141
1380.45
1390.112
140.462
1400.542
1410.314
1420.302
1430.0334
1440.814
1450.24
1460.0979
1470.108
1480.123
1490.267
150.13
1500.549
1510.927
1520.374
1530.432
1540.896
1550.0075
1560.398
1570.244
1580.1
1590.177
160.936
1600.272
1610.067
1620.8
1630.297
1640.614
1650.619
1660.477
1670.143
1680.196
1690.55
170.922
180.623
190.74
20.771
200.66
210.641
220.871
230.678
240.495
250.0304
260.16
270.224
280.421
290.0582
30.0499
300.417
310.749
320.232
330.517
340.955
350.109
360.0239
370.199
380.325
390.393
40.613
400.242
410.169
420.113
430.156
440.389
450.962
460.181
470.0788
480.163
490.0998
50.358
500.792
510.462
520.425
530.515
540.836
550.0955
560.749
570.384
580.0239
590.343
60.851
600.491
610.0499
620.0296
630.77
640.224
650.691
660.638
670.461
680.689
690.655
70.138
700.095
710.0403
720.0681
730.758
740.182
750.0115
760.0698
770.533
780.175
790.705
80.495
800.0111
810.166
820.162
830.658
840.436
850.593
860.126
870.266
880.657
890.927
90.485
900.0284
910.53
920.356
930.825
940.0483
950.00953
960.618
970.391
980.116
990.0396



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: CNhs12181


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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