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FF:12171-128I2: 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, 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 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 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-Basophils0.18
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.157
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-0.252
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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-Whole0.0262
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-Whole0.822
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: CNhs12199

Jaspar motifP-value
MA0002.25.1957e-10
MA0003.10.572
MA0004.10.85
MA0006.10.284
MA0007.10.774
MA0009.10.136
MA0014.10.841
MA0017.10.0221
MA0018.20.547
MA0019.10.383
MA0024.10.32
MA0025.10.576
MA0027.10.997
MA0028.11.16797e-7
MA0029.10.798
MA0030.10.177
MA0031.10.00828
MA0035.20.0993
MA0038.10.0811
MA0039.20.759
MA0040.10.44
MA0041.10.11
MA0042.10.197
MA0043.10.158
MA0046.10.749
MA0047.20.0833
MA0048.10.193
MA0050.12.59366e-9
MA0051.11.04924e-4
MA0052.10.0102
MA0055.10.552
MA0057.10.725
MA0058.10.587
MA0059.10.555
MA0060.10.12
MA0061.10.00277
MA0062.26.92447e-26
MA0065.20.0405
MA0066.10.269
MA0067.10.986
MA0068.10.827
MA0069.10.869
MA0070.10.569
MA0071.10.581
MA0072.10.227
MA0073.10.843
MA0074.10.564
MA0076.11.58655e-12
MA0077.10.0286
MA0078.10.773
MA0079.20.678
MA0080.25.59758e-14
MA0081.10.00606
MA0083.10.0123
MA0084.10.636
MA0087.10.757
MA0088.10.038
MA0090.12.46521e-4
MA0091.10.868
MA0092.10.821
MA0093.10.873
MA0099.20.00923
MA0100.10.345
MA0101.10.564
MA0102.20.505
MA0103.10.108
MA0104.20.152
MA0105.15.6878e-5
MA0106.10.128
MA0107.10.668
MA0108.27.99161e-13
MA0111.10.265
MA0112.20.366
MA0113.10.467
MA0114.10.24
MA0115.10.762
MA0116.13.26428e-5
MA0117.10.722
MA0119.10.3
MA0122.10.2
MA0124.10.375
MA0125.10.656
MA0131.10.551
MA0135.10.903
MA0136.11.24155e-27
MA0137.20.00779
MA0138.20.887
MA0139.10.00472
MA0140.10.162
MA0141.10.881
MA0142.10.458
MA0143.10.309
MA0144.10.087
MA0145.10.804
MA0146.10.373
MA0147.10.187
MA0148.10.271
MA0149.10.311
MA0150.10.182
MA0152.10.0164
MA0153.10.681
MA0154.10.0083
MA0155.10.736
MA0156.11.27011e-29
MA0157.10.00884
MA0159.10.0733
MA0160.10.448
MA0162.10.783
MA0163.11.13747e-9
MA0164.10.582
MA0258.10.457
MA0259.10.416



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: CNhs12199

Novel motifP-value
10.327
100.0249
1000.563
1010.364
1020.632
1030.0609
1040.616
1050.0941
1060.574
1070.0407
1080.6
1090.0863
110.124
1100.519
1110.308
1120.422
1130.254
1140.333
1150.214
1160.483
1170.00594
1180.524
1190.798
120.612
1200.287
1210.883
1220.338
1230.463
1240.114
1250.817
1260.179
1270.309
1280.65
1290.176
130.714
1300.703
1310.591
1320.705
1330.688
1340.654
1350.352
1360.937
1370.0884
1380.223
1390.0594
140.4
1400.321
1410.987
1420.5
1432.34936e-4
1440.748
1450.572
1460.193
1470.0113
1480.182
1490.888
150.0945
1500.905
1510.486
1520.2
1530.688
1540.8
1550.0599
1560.739
1570.373
1580.245
1590.13
160.949
1600.906
1610.255
1620.119
1630.758
1640.429
1650.456
1660.638
1670.515
1680.0489
1690.981
170.828
180.734
190.29
20.535
200.879
210.599
220.876
230.577
240.682
250.0315
260.914
270.0143
280.34
290.103
30.0533
300.726
310.838
320.0856
330.445
340.718
350.116
360.0727
370.239
380.574
390.366
40.684
400.746
410.103
420.0586
430.304
440.541
450.91
460.208
470.0996
480.19
490.207
50.142
500.465
510.569
520.186
530.31
540.629
550.298
560.598
570.84
580.0404
590.245
60.692
600.453
610.0948
620.0266
630.943
640.264
650.932
660.852
670.845
680.596
690.649
70.192
700.0402
710.17
720.0427
730.919
740.321
750.0307
760.248
770.557
780.133
790.24
80.706
800.00121
810.418
820.0663
830.731
840.661
850.592
860.182
870.728
880.625
890.889
90.392
900.0409
910.966
920.449
930.189
940.108
950.0178
960.123
970.438
980.207
990.051



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: CNhs12199


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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