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FF:12204-129C8: 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, donation1
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-0.0859
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-0.205
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: CNhs12183

Jaspar motifP-value
MA0002.21.17423e-5
MA0003.10.645
MA0004.10.487
MA0006.10.437
MA0007.10.725
MA0009.10.691
MA0014.10.552
MA0017.10.119
MA0018.20.337
MA0019.10.896
MA0024.10.746
MA0025.10.898
MA0027.10.54
MA0028.11.9634e-6
MA0029.10.383
MA0030.10.0137
MA0031.10.0236
MA0035.20.279
MA0038.10.604
MA0039.20.404
MA0040.10.828
MA0041.10.187
MA0042.10.824
MA0043.10.367
MA0046.10.667
MA0047.20.336
MA0048.10.408
MA0050.11.16501e-11
MA0051.17.27103e-6
MA0052.10.133
MA0055.10.454
MA0057.10.729
MA0058.10.291
MA0059.10.387
MA0060.10.759
MA0061.11.07739e-5
MA0062.25.52484e-19
MA0065.20.0855
MA0066.10.585
MA0067.10.341
MA0068.10.366
MA0069.10.382
MA0070.10.462
MA0071.10.757
MA0072.10.633
MA0073.10.559
MA0074.10.727
MA0076.11.84616e-11
MA0077.10.29
MA0078.10.667
MA0079.20.574
MA0080.24.08716e-12
MA0081.12.09329e-4
MA0083.10.215
MA0084.10.39
MA0087.10.298
MA0088.10.0863
MA0090.16.51167e-5
MA0091.10.76
MA0092.10.72
MA0093.10.544
MA0099.21.73585e-4
MA0100.10.245
MA0101.10.00191
MA0102.20.288
MA0103.10.0119
MA0104.20.117
MA0105.12.20053e-7
MA0106.10.314
MA0107.10.00142
MA0108.23.96136e-7
MA0111.10.477
MA0112.20.0861
MA0113.10.94
MA0114.10.22
MA0115.10.379
MA0116.13.57123e-5
MA0117.10.594
MA0119.10.36
MA0122.10.183
MA0124.10.538
MA0125.10.741
MA0131.10.0464
MA0135.10.0566
MA0136.12.03528e-19
MA0137.20.445
MA0138.20.773
MA0139.10.265
MA0140.10.062
MA0141.10.888
MA0142.10.175
MA0143.10.895
MA0144.10.909
MA0145.10.783
MA0146.10.267
MA0147.10.142
MA0148.10.798
MA0149.10.18
MA0150.10.529
MA0152.10.281
MA0153.10.0103
MA0154.19.65775e-4
MA0155.10.677
MA0156.13.29066e-17
MA0157.10.0869
MA0159.10.0494
MA0160.10.429
MA0162.10.975
MA0163.17.99887e-9
MA0164.10.843
MA0258.10.213
MA0259.10.517



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: CNhs12183

Novel motifP-value
10.151
100.0358
1000.521
1010.305
1020.887
1030.0766
1040.158
1050.405
1060.59
1070.261
1080.239
1090.111
110.127
1100.172
1110.167
1120.158
1130.0104
1140.435
1150.842
1160.618
1170.00104
1180.19
1190.848
120.808
1200.629
1210.412
1220.444
1230.093
1240.109
1250.139
1260.114
1270.644
1280.43
1290.759
130.514
1300.382
1310.488
1320.263
1330.00816
1340.584
1350.816
1360.507
1370.0475
1380.43
1390.0905
140.299
1400.484
1410.252
1420.509
1430.0673
1440.723
1450.297
1460.128
1470.0582
1480.663
1490.474
150.158
1500.556
1510.852
1520.575
1530.655
1540.857
1550.0168
1560.29
1570.162
1580.0954
1590.179
160.825
1600.532
1610.045
1620.556
1630.268
1640.499
1650.28
1660.539
1670.12
1680.203
1690.599
170.984
180.814
190.649
20.848
200.606
210.758
220.765
230.553
240.33
250.0264
260.261
270.246
280.303
290.111
30.0874
300.346
310.744
320.122
330.36
340.847
350.194
360.0371
370.119
380.396
390.451
40.704
400.177
410.145
420.139
430.201
440.57
450.926
460.237
470.0829
480.152
490.183
50.477
500.979
510.505
520.481
530.397
540.973
550.106
560.676
570.53
580.0202
590.352
60.863
600.519
610.0352
620.0312
630.766
640.36
650.862
660.79
670.402
680.237
690.585
70.126
700.228
710.0561
720.0566
730.527
740.469
750.0111
760.0368
770.535
780.27
790.223
80.848
800.013
810.262
820.14
830.866
840.286
850.819
860.132
870.0879
880.669
890.912
90.43
900.0148
910.718
920.562
930.772
940.08
950.0109
960.465
970.464
980.117
990.0182



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: CNhs12183


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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