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FF:12194-129B7: 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, donation2
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-0.0413
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
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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: CNhs12179

Jaspar motifP-value
MA0002.23.84597e-6
MA0003.10.498
MA0004.10.485
MA0006.10.413
MA0007.10.413
MA0009.10.921
MA0014.10.781
MA0017.10.0337
MA0018.20.834
MA0019.10.997
MA0024.10.686
MA0025.10.114
MA0027.10.459
MA0028.12.23461e-5
MA0029.10.778
MA0030.10.0213
MA0031.10.0341
MA0035.20.495
MA0038.10.265
MA0039.20.482
MA0040.10.762
MA0041.10.21
MA0042.10.994
MA0043.10.607
MA0046.10.981
MA0047.20.244
MA0048.10.439
MA0050.12.05256e-12
MA0051.11.15711e-6
MA0052.10.671
MA0055.10.568
MA0057.10.777
MA0058.10.385
MA0059.10.385
MA0060.10.578
MA0061.11.88873e-5
MA0062.21.59819e-15
MA0065.20.033
MA0066.10.491
MA0067.10.678
MA0068.10.432
MA0069.10.545
MA0070.10.296
MA0071.10.896
MA0072.10.864
MA0073.10.693
MA0074.10.785
MA0076.18.43056e-9
MA0077.10.304
MA0078.10.597
MA0079.20.576
MA0080.23.81202e-12
MA0081.11.93979e-4
MA0083.10.0156
MA0084.10.333
MA0087.10.324
MA0088.10.111
MA0090.11.39102e-4
MA0091.10.784
MA0092.10.995
MA0093.10.592
MA0099.27.41371e-6
MA0100.10.169
MA0101.10.0129
MA0102.20.338
MA0103.10.00544
MA0104.20.144
MA0105.11.56102e-7
MA0106.10.393
MA0107.10.00578
MA0108.23.41759e-9
MA0111.10.311
MA0112.20.047
MA0113.10.907
MA0114.10.106
MA0115.10.189
MA0116.11.28306e-5
MA0117.10.733
MA0119.10.666
MA0122.10.236
MA0124.10.889
MA0125.10.859
MA0131.10.127
MA0135.10.0508
MA0136.12.99144e-18
MA0137.20.804
MA0138.20.753
MA0139.10.16
MA0140.10.149
MA0141.10.928
MA0142.10.2
MA0143.10.586
MA0144.10.665
MA0145.10.816
MA0146.10.152
MA0147.10.132
MA0148.10.646
MA0149.10.119
MA0150.10.312
MA0152.10.283
MA0153.10.0445
MA0154.12.29679e-4
MA0155.10.636
MA0156.12.04043e-15
MA0157.10.0898
MA0159.10.0763
MA0160.10.579
MA0162.10.934
MA0163.14.62056e-9
MA0164.10.684
MA0258.10.159
MA0259.10.52



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: CNhs12179

Novel motifP-value
10.104
100.0263
1000.613
1010.126
1020.834
1030.122
1040.174
1050.418
1060.699
1070.286
1080.455
1090.0771
110.0936
1100.102
1110.101
1120.308
1130.0229
1140.358
1150.928
1160.712
1170.00158
1180.209
1190.722
120.94
1200.738
1210.259
1220.55
1230.0346
1240.216
1250.168
1260.207
1270.597
1280.436
1290.689
130.443
1300.349
1310.604
1320.373
1330.00539
1340.787
1350.665
1360.438
1370.109
1380.334
1390.119
140.306
1400.243
1410.153
1420.368
1430.0864
1440.893
1450.227
1460.199
1470.0661
1480.137
1490.399
150.134
1500.673
1510.644
1520.688
1530.854
1540.999
1550.00762
1560.47
1570.251
1580.196
1590.132
160.764
1600.447
1610.0785
1620.637
1630.26
1640.438
1650.114
1660.421
1670.126
1680.105
1690.507
170.9
180.652
190.694
20.811
200.575
210.698
220.753
230.535
240.386
250.0328
260.222
270.278
280.452
290.102
30.0461
300.373
310.701
320.239
330.635
340.766
350.111
360.0346
370.164
380.465
390.405
40.562
400.255
410.191
420.0978
430.16
440.596
450.94
460.155
470.0747
480.107
490.0993
50.468
500.947
510.557
520.424
530.293
540.713
550.0406
560.621
570.422
580.023
590.319
60.975
600.592
610.0257
620.0245
630.76
640.252
650.822
660.747
670.304
680.461
690.602
70.143
700.168
710.0335
720.0422
730.506
740.39
750.00699
760.0697
770.63
780.165
790.334
80.542
800.00345
810.2
820.112
830.838
840.257
850.933
860.0863
870.171
880.59
890.716
90.533
900.0408
910.503
920.713
930.877
940.036
950.00476
960.471
970.451
980.233
990.0655



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: CNhs12179


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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