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FF:12148-128F6: 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 17:14, 29 March 2012


Name:CD8+ T Cells (pluriselect), donor090325, 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
sexmale
ageNA
cell typeT cell, CD8+
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 typetotal RNA
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-Basophils0.162
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.19
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-0.223
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.0609
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-Whole0.73
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: CNhs12201

Jaspar motifP-value
MA0002.21.22595e-9
MA0003.10.491
MA0004.10.689
MA0006.10.29
MA0007.10.676
MA0009.10.251
MA0014.10.81
MA0017.10.0358
MA0018.20.304
MA0019.10.516
MA0024.10.243
MA0025.10.346
MA0027.10.67
MA0028.12.4628e-7
MA0029.10.919
MA0030.10.0252
MA0031.10.00235
MA0035.20.155
MA0038.10.18
MA0039.20.456
MA0040.10.224
MA0041.10.229
MA0042.10.206
MA0043.10.263
MA0046.10.547
MA0047.20.0231
MA0048.10.189
MA0050.16.78281e-10
MA0051.12.88432e-5
MA0052.10.0493
MA0055.10.634
MA0057.10.604
MA0058.10.396
MA0059.10.516
MA0060.10.185
MA0061.11.28376e-4
MA0062.24.13705e-26
MA0065.20.0469
MA0066.10.369
MA0067.10.21
MA0068.10.388
MA0069.10.687
MA0070.10.358
MA0071.10.835
MA0072.10.278
MA0073.10.808
MA0074.10.718
MA0076.13.51631e-12
MA0077.10.0518
MA0078.10.706
MA0079.20.935
MA0080.21.9682e-14
MA0081.10.00164
MA0083.10.0349
MA0084.10.587
MA0087.10.516
MA0088.10.0413
MA0090.14.64849e-4
MA0091.10.99
MA0092.10.853
MA0093.10.688
MA0099.20.159
MA0100.10.348
MA0101.10.0465
MA0102.20.0659
MA0103.10.232
MA0104.20.122
MA0105.11.61252e-5
MA0106.10.181
MA0107.10.0513
MA0108.28.998e-9
MA0111.10.274
MA0112.20.504
MA0113.10.718
MA0114.10.339
MA0115.10.811
MA0116.16.97936e-5
MA0117.10.542
MA0119.10.302
MA0122.10.188
MA0124.10.607
MA0125.10.545
MA0131.10.35
MA0135.10.511
MA0136.18.19029e-28
MA0137.20.00216
MA0138.20.99
MA0139.10.00597
MA0140.10.187
MA0141.10.782
MA0142.10.641
MA0143.10.445
MA0144.10.0561
MA0145.10.702
MA0146.10.329
MA0147.10.214
MA0148.10.147
MA0149.10.36
MA0150.10.526
MA0152.10.0208
MA0153.10.574
MA0154.10.00789
MA0155.10.773
MA0156.11.68776e-31
MA0157.10.00485
MA0159.10.185
MA0160.10.413
MA0162.10.942
MA0163.14.77974e-9
MA0164.10.587
MA0258.10.674
MA0259.10.442



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: CNhs12201

Novel motifP-value
10.451
100.0303
1000.704
1010.349
1020.694
1030.103
1040.541
1050.125
1060.74
1070.0366
1080.489
1090.0743
110.151
1100.592
1110.472
1120.444
1130.18
1140.336
1150.28
1160.369
1170.00334
1180.466
1190.932
120.46
1200.5
1210.874
1220.367
1230.697
1240.181
1250.828
1260.148
1270.321
1280.81
1290.221
130.614
1300.865
1310.354
1320.526
1330.981
1340.639
1350.417
1360.913
1370.0264
1380.218
1390.0745
140.327
1400.226
1410.871
1420.827
1433.76691e-4
1440.798
1450.551
1460.239
1470.0127
1480.242
1490.921
150.133
1500.996
1510.435
1520.33
1530.882
1540.816
1550.0616
1560.841
1570.31
1580.151
1590.114
160.939
1600.791
1610.19
1620.12
1630.874
1640.416
1650.589
1660.678
1670.534
1680.0274
1690.993
170.885
180.818
190.228
20.666
200.959
210.736
220.855
230.653
240.599
250.0333
260.981
270.024
280.317
290.0529
30.0715
300.608
310.788
320.065
330.332
340.788
350.0922
360.0581
370.232
380.656
390.345
40.825
400.63
410.0364
420.0726
430.34
440.645
450.896
460.317
470.0964
480.254
490.265
50.103
500.522
510.579
520.204
530.312
540.638
550.435
560.729
570.857
580.0528
590.35
60.707
600.431
610.071
620.0347
630.938
640.285
650.89
660.909
670.886
680.698
690.694
70.179
700.0388
710.147
720.061
730.615
740.36
750.0252
760.279
770.436
780.389
790.511
80.682
806.56502e-4
810.46
820.187
830.836
840.758
850.669
860.14
870.377
880.652
890.727
90.378
900.0425
910.904
920.634
930.233
940.112
950.0115
960.187
970.53
980.171
990.0176



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: CNhs12201


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)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000625 (CD8-positive, alpha-beta T cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T 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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