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FF:12209-129D4: 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, 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-0.1
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-0.28
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12185

Jaspar motifP-value
MA0002.28.59857e-6
MA0003.10.346
MA0004.10.372
MA0006.10.538
MA0007.10.496
MA0009.10.951
MA0014.10.722
MA0017.10.0195
MA0018.20.983
MA0019.10.591
MA0024.10.996
MA0025.10.424
MA0027.10.431
MA0028.13.2637e-5
MA0029.10.488
MA0030.10.00943
MA0031.10.0387
MA0035.20.346
MA0038.10.348
MA0039.20.341
MA0040.10.884
MA0041.10.135
MA0042.10.713
MA0043.10.663
MA0046.10.333
MA0047.20.183
MA0048.10.472
MA0050.11.45038e-11
MA0051.11.28158e-5
MA0052.10.0991
MA0055.10.617
MA0057.10.814
MA0058.10.235
MA0059.10.343
MA0060.10.584
MA0061.15.7299e-5
MA0062.22.85816e-15
MA0065.20.0188
MA0066.10.249
MA0067.10.563
MA0068.10.364
MA0069.10.265
MA0070.10.467
MA0071.10.595
MA0072.10.611
MA0073.10.451
MA0074.10.666
MA0076.16.66016e-9
MA0077.10.274
MA0078.10.699
MA0079.20.518
MA0080.22.80955e-12
MA0081.16.61575e-4
MA0083.10.073
MA0084.10.521
MA0087.10.6
MA0088.10.115
MA0090.11.14564e-4
MA0091.10.5
MA0092.10.999
MA0093.10.456
MA0099.28.53768e-5
MA0100.10.213
MA0101.10.00456
MA0102.20.441
MA0103.10.00407
MA0104.20.139
MA0105.15.77482e-7
MA0106.10.419
MA0107.10.00305
MA0108.28.38861e-8
MA0111.10.342
MA0112.20.0115
MA0113.10.959
MA0114.10.0633
MA0115.10.321
MA0116.11.68915e-5
MA0117.10.822
MA0119.10.62
MA0122.10.296
MA0124.10.833
MA0125.10.963
MA0131.10.16
MA0135.10.0553
MA0136.11.2912e-18
MA0137.20.456
MA0138.20.375
MA0139.10.165
MA0140.10.135
MA0141.10.844
MA0142.10.114
MA0143.10.913
MA0144.10.884
MA0145.10.963
MA0146.10.205
MA0147.10.144
MA0148.10.829
MA0149.10.0875
MA0150.10.596
MA0152.10.199
MA0153.10.0792
MA0154.12.98064e-4
MA0155.10.796
MA0156.12.16551e-15
MA0157.10.0711
MA0159.10.0345
MA0160.10.343
MA0162.10.754
MA0163.13.57029e-9
MA0164.10.913
MA0258.10.077
MA0259.10.508



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: CNhs12185

Novel motifP-value
10.0937
100.0493
1000.595
1010.392
1020.68
1030.113
1040.174
1050.262
1060.663
1070.361
1080.362
1090.0587
110.087
1100.199
1110.104
1120.239
1130.0365
1140.354
1150.817
1160.864
1170.00231
1180.2
1190.998
120.816
1200.561
1210.356
1220.32
1230.103
1240.0984
1250.346
1260.11
1270.533
1280.558
1290.718
130.402
1300.358
1310.716
1320.346
1330.00482
1340.523
1350.342
1360.416
1370.0633
1380.355
1390.0702
140.359
1400.672
1410.253
1420.72
1430.0369
1440.752
1450.211
1460.163
1470.0815
1480.143
1490.53
150.207
1500.711
1510.439
1520.856
1530.65
1540.776
1550.00795
1560.385
1570.263
1580.141
1590.184
160.98
1600.284
1610.114
1620.993
1630.206
1640.596
1650.255
1660.258
1670.14
1680.147
1690.443
170.94
180.548
190.883
20.972
200.792
210.816
220.725
230.695
240.321
250.0353
260.182
270.242
280.513
290.0668
30.0371
300.454
310.732
320.27
330.376
340.755
350.174
360.0252
370.11
380.364
390.52
40.576
400.154
410.177
420.0822
430.155
440.391
450.88
460.203
470.0738
480.111
490.122
50.307
500.978
510.463
520.448
530.376
540.844
550.119
560.591
570.63
580.0161
590.266
60.848
600.582
610.0294
620.0178
630.681
640.214
650.565
660.712
670.361
680.729
690.757
70.123
700.128
710.0497
720.0401
730.504
740.372
750.00773
760.0891
770.812
780.146
790.443
80.538
800.00255
810.183
820.0824
830.561
840.329
850.813
860.105
870.0965
880.723
890.829
90.363
900.0475
910.842
920.546
930.736
940.0357
950.00616
960.501
970.556
980.0864
990.103



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: CNhs12185


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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