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FF:12206-129D1: 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), donor090612, 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-Basophils0.168
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.165
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-0.224
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.0923
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-Whole0.84
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: CNhs12184

Jaspar motifP-value
MA0002.22.89832e-10
MA0003.10.482
MA0004.10.944
MA0006.10.508
MA0007.10.954
MA0009.10.202
MA0014.10.98
MA0017.10.0292
MA0018.20.431
MA0019.10.992
MA0024.10.219
MA0025.10.71
MA0027.10.929
MA0028.11.18661e-4
MA0029.10.697
MA0030.10.138
MA0031.10.00834
MA0035.20.212
MA0038.10.0976
MA0039.20.898
MA0040.10.884
MA0041.10.861
MA0042.10.559
MA0043.10.325
MA0046.10.795
MA0047.20.175
MA0048.10.28
MA0050.14.61348e-9
MA0051.16.31316e-5
MA0052.10.00109
MA0055.10.394
MA0057.10.685
MA0058.10.81
MA0059.10.547
MA0060.10.0437
MA0061.10.00469
MA0062.24.28177e-18
MA0065.20.0386
MA0066.10.157
MA0067.10.643
MA0068.10.424
MA0069.10.747
MA0070.10.411
MA0071.10.696
MA0072.10.439
MA0073.10.797
MA0074.10.642
MA0076.11.18089e-7
MA0077.10.0862
MA0078.10.751
MA0079.20.563
MA0080.22.80608e-15
MA0081.10.00427
MA0083.10.0353
MA0084.10.449
MA0087.10.652
MA0088.10.0603
MA0090.12.86221e-4
MA0091.10.844
MA0092.10.921
MA0093.10.975
MA0099.20.0394
MA0100.10.512
MA0101.10.675
MA0102.20.286
MA0103.10.148
MA0104.20.277
MA0105.11.08006e-5
MA0106.10.355
MA0107.10.844
MA0108.21.57164e-10
MA0111.10.207
MA0112.20.0863
MA0113.10.706
MA0114.10.271
MA0115.10.774
MA0116.11.02917e-5
MA0117.10.725
MA0119.10.715
MA0122.10.23
MA0124.10.491
MA0125.10.308
MA0131.10.603
MA0135.10.829
MA0136.11.19946e-27
MA0137.20.0105
MA0138.20.995
MA0139.10.0103
MA0140.10.213
MA0141.10.984
MA0142.10.568
MA0143.10.377
MA0144.10.0949
MA0145.10.943
MA0146.10.3
MA0147.10.31
MA0148.10.404
MA0149.10.234
MA0150.10.653
MA0152.10.037
MA0153.10.261
MA0154.10.00443
MA0155.10.769
MA0156.11.58714e-27
MA0157.10.00938
MA0159.10.0574
MA0160.10.401
MA0162.10.906
MA0163.13.775e-10
MA0164.10.39
MA0258.10.121
MA0259.10.689



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: CNhs12184

Novel motifP-value
10.189
100.0185
1000.792
1010.277
1020.525
1030.151
1040.533
1050.0874
1060.511
1070.243
1080.645
1090.0616
110.0778
1100.44
1110.358
1120.449
1130.143
1140.206
1150.307
1160.929
1170.00656
1180.307
1190.71
120.654
1200.494
1210.913
1220.432
1230.041
1240.0963
1250.699
1260.262
1270.294
1280.635
1290.359
130.65
1300.751
1310.784
1320.838
1330.753
1340.753
1350.249
1360.934
1370.0445
1380.204
1390.0171
140.256
1400.0921
1410.636
1420.557
1431.37755e-5
1440.744
1450.383
1460.226
1470.0179
1480.114
1490.883
150.0825
1500.74
1510.28
1520.54
1530.8
1540.949
1550.0239
1560.479
1570.352
1580.283
1590.0878
160.728
1600.581
1610.298
1620.282
1630.816
1640.417
1650.252
1660.663
1670.55
1680.0991
1690.445
170.742
180.603
190.656
20.538
200.738
210.309
220.781
230.947
240.407
250.0544
260.56
270.0397
280.395
290.125
30.0294
300.586
310.648
320.133
330.483
340.659
350.0722
360.0514
370.21
380.549
390.562
40.797
400.539
410.15
420.0515
430.226
440.535
450.958
460.125
470.0822
480.128
490.142
50.186
500.614
510.512
520.467
530.143
540.447
550.22
560.494
570.625
580.0327
590.259
60.96
600.245
610.131
620.0165
630.649
640.192
650.613
660.99
670.928
680.518
690.92
70.194
700.0172
710.106
720.0747
730.605
740.334
750.0356
760.295
770.698
780.161
790.408
80.878
800.00167
810.309
820.0942
830.984
840.395
850.733
860.156
870.607
880.775
890.876
90.358
900.0107
910.895
920.29
930.223
940.0625
950.0229
960.128
970.442
980.236
990.138



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: CNhs12184


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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