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FF:12191-129B4: 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:CD8+ T Cells (pluriselect), donor090309, 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 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)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-Basophils0.218
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.168
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-0.245
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-Whole0.876
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: CNhs12178

Jaspar motifP-value
MA0002.25.47488e-9
MA0003.10.829
MA0004.10.769
MA0006.10.36
MA0007.10.914
MA0009.10.296
MA0014.10.984
MA0017.10.05
MA0018.20.383
MA0019.10.998
MA0024.10.253
MA0025.10.249
MA0027.10.966
MA0028.12.47524e-5
MA0029.10.795
MA0030.10.261
MA0031.10.011
MA0035.20.0819
MA0038.10.0264
MA0039.20.757
MA0040.10.889
MA0041.10.651
MA0042.10.966
MA0043.10.0248
MA0046.10.947
MA0047.20.0525
MA0048.10.416
MA0050.19.70763e-6
MA0051.10.016
MA0052.10.00237
MA0055.10.921
MA0057.10.948
MA0058.10.793
MA0059.10.298
MA0060.10.0516
MA0061.10.00831
MA0062.22.41851e-16
MA0065.20.0148
MA0066.10.0996
MA0067.10.463
MA0068.10.874
MA0069.10.997
MA0070.10.494
MA0071.10.383
MA0072.10.346
MA0073.10.901
MA0074.10.635
MA0076.12.21013e-8
MA0077.10.238
MA0078.10.493
MA0079.20.38
MA0080.21.64526e-12
MA0081.10.019
MA0083.10.00725
MA0084.10.487
MA0087.10.86
MA0088.10.0593
MA0090.17.13086e-4
MA0091.10.889
MA0092.10.846
MA0093.10.894
MA0099.20.0286
MA0100.10.401
MA0101.10.871
MA0102.20.581
MA0103.10.0799
MA0104.20.0765
MA0105.15.25427e-6
MA0106.10.571
MA0107.10.908
MA0108.21.72104e-12
MA0111.10.195
MA0112.20.0921
MA0113.10.342
MA0114.10.123
MA0115.10.649
MA0116.12.27644e-5
MA0117.10.796
MA0119.10.938
MA0122.10.26
MA0124.10.596
MA0125.10.54
MA0131.10.405
MA0135.10.38
MA0136.11.4093e-23
MA0137.20.0445
MA0138.20.987
MA0139.10.0019
MA0140.10.12
MA0141.10.659
MA0142.10.437
MA0143.10.302
MA0144.10.262
MA0145.10.729
MA0146.10.419
MA0147.10.084
MA0148.10.113
MA0149.10.107
MA0150.10.314
MA0152.10.0579
MA0153.10.34
MA0154.10.00434
MA0155.10.904
MA0156.11.51027e-20
MA0157.10.00447
MA0159.10.045
MA0160.10.323
MA0162.10.835
MA0163.12.89845e-12
MA0164.10.613
MA0258.10.124
MA0259.10.258



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: CNhs12178

Novel motifP-value
10.201
100.0147
1000.982
1010.158
1020.542
1030.256
1040.441
1050.0916
1060.843
1070.265
1080.858
1090.0379
110.056
1100.424
1110.304
1120.374
1130.298
1140.193
1150.183
1160.953
1170.00554
1180.385
1190.578
120.738
1200.55
1210.969
1220.429
1230.0244
1240.0224
1250.625
1260.364
1270.654
1280.796
1290.139
130.501
1301
1310.821
1320.961
1330.979
1340.954
1350.358
1360.739
1370.268
1380.378
1390.0153
140.363
1400.103
1410.587
1420.314
1432.67382e-5
1440.674
1450.241
1460.12
1470.0327
1480.12
1490.994
150.0508
1500.539
1510.319
1520.238
1530.547
1540.96
1550.0145
1560.323
1570.574
1580.157
1590.208
160.628
1600.61
1610.229
1620.527
1630.607
1640.432
1650.639
1660.56
1670.183
1680.121
1690.672
170.848
180.618
190.551
20.668
200.921
210.425
220.891
230.84
240.789
250.0625
260.398
270.058
280.524
290.0478
30.0461
300.488
310.733
320.334
330.575
340.88
350.0663
360.0255
370.148
380.48
390.623
40.563
400.58
410.168
420.042
430.188
440.66
450.835
460.129
470.0526
480.126
490.0958
50.0999
500.513
510.434
520.28
530.183
540.395
550.293
560.501
570.342
580.0452
590.388
60.92
600.455
610.101
620.0212
630.605
640.178
650.623
660.891
670.956
680.664
690.871
70.149
700.00472
710.0974
720.0587
730.687
740.374
750.0246
760.342
770.604
780.11
790.273
80.649
800.00357
810.274
820.095
830.955
840.585
850.855
860.208
870.714
880.83
890.943
90.559
900.0089
910.865
920.268
930.277
940.0472
950.0171
960.0867
970.386
980.13
990.161



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: CNhs12178


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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