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FF:11383-118B6: 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 17:05, 29 March 2012


Name:CD8+ T Cells, donor3
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 stage53 years old adult
sexmale
age53
cell typet cell, CD8+
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCD8T727
catalog number3H100-26-10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Basophils0.157
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0387
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0445
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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-Whole0.591
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: CNhs11999

Jaspar motifP-value
MA0002.20.00358
MA0003.10.228
MA0004.10.938
MA0006.10.151
MA0007.10.302
MA0009.10.0382
MA0014.10.783
MA0017.10.112
MA0018.22.58713e-9
MA0019.10.449
MA0024.10.829
MA0025.10.199
MA0027.10.788
MA0028.10.0221
MA0029.10.569
MA0030.10.0511
MA0031.14.57072e-5
MA0035.20.328
MA0038.10.0335
MA0039.20.288
MA0040.10.564
MA0041.10.266
MA0042.10.649
MA0043.19.91629e-4
MA0046.10.0531
MA0047.20.607
MA0048.10.589
MA0050.11.09689e-4
MA0051.10.0838
MA0052.10.0227
MA0055.10.962
MA0057.10.189
MA0058.10.837
MA0059.10.684
MA0060.10.203
MA0061.11.64805e-7
MA0062.23.743e-10
MA0065.20.609
MA0066.10.937
MA0067.10.00448
MA0068.10.938
MA0069.10.782
MA0070.10.436
MA0071.10.886
MA0072.10.232
MA0073.10.645
MA0074.10.674
MA0076.10.00699
MA0077.10.146
MA0078.10.963
MA0079.20.833
MA0080.23.02463e-8
MA0081.10.0339
MA0083.10.268
MA0084.10.21
MA0087.10.666
MA0088.10.409
MA0090.13.20762e-4
MA0091.10.189
MA0092.10.718
MA0093.10.829
MA0099.20.0954
MA0100.10.955
MA0101.15.90001e-5
MA0102.20.774
MA0103.10.98
MA0104.20.547
MA0105.18.75803e-6
MA0106.10.0456
MA0107.11.23975e-4
MA0108.21.04148e-4
MA0111.10.487
MA0112.20.0786
MA0113.10.327
MA0114.10.144
MA0115.10.199
MA0116.10.298
MA0117.10.0365
MA0119.10.377
MA0122.10.897
MA0124.10.121
MA0125.10.124
MA0131.10.0387
MA0135.10.099
MA0136.11.79642e-13
MA0137.20.0851
MA0138.20.0356
MA0139.10.997
MA0140.10.725
MA0141.10.0767
MA0142.10.0889
MA0143.10.0689
MA0144.10.224
MA0145.10.0116
MA0146.10.724
MA0147.10.54
MA0148.10.988
MA0149.10.681
MA0150.10.742
MA0152.10.00232
MA0153.10.0886
MA0154.10.512
MA0155.10.146
MA0156.11.16077e-8
MA0157.10.00101
MA0159.10.854
MA0160.10.472
MA0162.10.164
MA0163.10.0379
MA0164.10.675
MA0258.10.725
MA0259.10.522



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: CNhs11999

Novel motifP-value
10.982
100.0123
1000.695
1010.153
1020.782
1030.127
1040.941
1050.774
1060.47
1070.0196
1080.636
1090.882
110.864
1100.37
1110.578
1120.643
1130.243
1140.855
1150.415
1160.196
1170.00834
1180.505
1190.388
120.727
1200.254
1210.662
1220.768
1237.15152e-7
1240.963
1250.689
1260.976
1270.456
1280.874
1290.274
130.561
1300.202
1310.263
1320.351
1330.998
1340.767
1350.161
1360.924
1370.0897
1380.774
1390.17
140.579
1400.418
1410.919
1420.23
1430.0751
1440.992
1450.522
1460.442
1470.0233
1480.508
1490.141
150.528
1500.806
1510.557
1520.533
1530.508
1540.106
1550.115
1560.859
1570.899
1580.00603
1590.864
160.2
1600.0631
1610.526
1620.0802
1630.622
1640.0967
1650.838
1660.455
1670.124
1680.384
1690.154
170.554
180.403
190.0259
20.132
200.105
210.758
220.144
230.417
240.379
250.245
260.817
270.442
280.428
290.167
30.63
300.0426
310.508
320.00827
330.62
340.299
350.387
360.15
370.634
380.613
390.373
40.956
400.769
410.272
420.384
430.882
440.504
450.0932
460.873
470.747
480.951
490.263
50.874
500.473
510.794
520.736
530.181
540.83
550.729
560.737
570.953
580.243
590.138
60.967
600.768
610.277
620.466
630.798
640.994
650.389
660.47
670.52
680.899
690.975
70.812
700.273
710.427
720.596
730.983
740.428
750.0725
760.0718
770.00251
780.891
790.772
80.291
800.154
810.889
820.631
830.883
840.107
850.917
860.102
870.559
880.986
890.00122
90.488
900.57
910.971
920.749
930.833
940.52
950.305
960.805
970.186
980.55
992.50252e-5



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: CNhs11999


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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