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FF:12174-128I5: 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 17:12, 29 March 2012


Name:CD19+ B Cells (pluriselect), donor090325, 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
sexmale
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)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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-0.12
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-0.22
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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: CNhs12175

Jaspar motifP-value
MA0002.22.51326e-5
MA0003.10.628
MA0004.10.335
MA0006.10.364
MA0007.10.613
MA0009.10.772
MA0014.10.768
MA0017.10.0334
MA0018.20.598
MA0019.10.841
MA0024.10.912
MA0025.10.279
MA0027.10.743
MA0028.19.85153e-7
MA0029.10.605
MA0030.10.0084
MA0031.10.0357
MA0035.20.42
MA0038.10.264
MA0039.20.517
MA0040.10.989
MA0041.10.136
MA0042.10.747
MA0043.10.961
MA0046.10.655
MA0047.20.17
MA0048.10.358
MA0050.11.0818e-11
MA0051.12.8725e-5
MA0052.10.25
MA0055.10.493
MA0057.10.762
MA0058.10.196
MA0059.10.371
MA0060.10.449
MA0061.16.56473e-5
MA0062.21.32625e-17
MA0065.20.0332
MA0066.10.644
MA0067.10.554
MA0068.10.0697
MA0069.10.557
MA0070.10.494
MA0071.10.628
MA0072.10.562
MA0073.10.578
MA0074.10.781
MA0076.17.74685e-11
MA0077.10.129
MA0078.10.713
MA0079.20.616
MA0080.21.89346e-11
MA0081.13.04906e-4
MA0083.10.00756
MA0084.10.295
MA0087.10.164
MA0088.10.127
MA0090.14.28915e-5
MA0091.10.719
MA0092.10.86
MA0093.10.387
MA0099.21.07687e-6
MA0100.10.189
MA0101.10.0117
MA0102.20.564
MA0103.10.0033
MA0104.20.1
MA0105.15.78948e-7
MA0106.10.443
MA0107.10.00542
MA0108.21.17452e-10
MA0111.10.432
MA0112.20.0891
MA0113.10.959
MA0114.10.0696
MA0115.10.0804
MA0116.12.1244e-5
MA0117.10.653
MA0119.10.41
MA0122.10.51
MA0124.10.821
MA0125.10.979
MA0131.10.0571
MA0135.10.0349
MA0136.15.77574e-18
MA0137.20.949
MA0138.20.734
MA0139.10.193
MA0140.10.25
MA0141.10.91
MA0142.10.226
MA0143.10.923
MA0144.10.568
MA0145.10.726
MA0146.10.155
MA0147.10.12
MA0148.10.676
MA0149.10.104
MA0150.10.181
MA0152.10.184
MA0153.10.0194
MA0154.14.77458e-4
MA0155.10.624
MA0156.16.68598e-16
MA0157.10.106
MA0159.10.0367
MA0160.10.416
MA0162.10.883
MA0163.11.3282e-9
MA0164.10.63
MA0258.10.227
MA0259.10.393



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: CNhs12175

Novel motifP-value
10.0885
100.0222
1000.671
1010.252
1020.956
1030.0556
1040.163
1050.507
1060.948
1070.183
1080.215
1090.0833
110.127
1100.272
1110.0713
1120.426
1130.027
1140.515
1150.972
1160.734
1170.00109
1180.14
1190.71
120.919
1200.709
1210.308
1220.458
1230.0579
1240.082
1250.203
1260.425
1270.614
1280.377
1290.996
130.426
1300.326
1310.54
1320.294
1330.0125
1340.838
1350.768
1360.449
1370.142
1380.381
1390.43
140.398
1400.273
1410.225
1420.28
1430.151
1440.693
1450.519
1460.0971
1470.0527
1480.405
1490.338
150.119
1500.621
1510.691
1520.6
1530.854
1540.914
1550.00728
1560.342
1570.285
1580.0869
1590.172
160.952
1600.571
1610.0787
1620.53
1630.178
1640.412
1650.439
1660.498
1670.102
1680.0981
1690.565
170.797
180.713
190.524
20.793
200.511
210.798
220.778
230.382
240.671
250.0268
260.382
270.21
280.423
290.0537
30.0607
300.326
310.714
320.248
330.444
340.909
350.153
360.0256
370.123
380.495
390.341
40.689
400.218
410.169
420.134
430.199
440.389
450.966
460.209
470.0772
480.167
490.134
50.443
500.975
510.513
520.371
530.474
540.813
550.119
560.791
570.492
580.025
590.381
60.655
600.752
610.0285
620.037
630.837
640.415
650.956
660.861
670.278
680.882
690.874
70.153
700.258
710.0478
720.0204
730.638
740.602
750.0044
760.0387
770.469
780.126
790.446
80.855
800.00457
810.143
820.248
830.751
840.341
850.946
860.0801
870.107
880.655
890.809
90.625
900.0265
910.88
920.663
930.845
940.0496
950.00516
960.781
970.446
980.279
990.0319



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: CNhs12175


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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