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FF:12186-129A8: 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 17:12, 29 March 2012


Name:CD8+ T Cells (pluriselect), donor090309, 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
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-Basophils0.12
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.155
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-0.242
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
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-Whole0.762
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: CNhs12176

Jaspar motifP-value
MA0002.23.18073e-9
MA0003.10.757
MA0004.10.763
MA0006.10.401
MA0007.10.935
MA0009.10.388
MA0014.10.803
MA0017.10.0335
MA0018.20.746
MA0019.10.69
MA0024.10.396
MA0025.10.789
MA0027.10.95
MA0028.11.75598e-6
MA0029.10.68
MA0030.10.144
MA0031.10.00266
MA0035.20.143
MA0038.10.11
MA0039.20.946
MA0040.10.937
MA0041.10.661
MA0042.10.868
MA0043.10.282
MA0046.10.985
MA0047.20.1
MA0048.10.424
MA0050.11.04257e-7
MA0051.18.44592e-4
MA0052.10.0093
MA0055.10.763
MA0057.10.581
MA0058.10.587
MA0059.10.378
MA0060.10.124
MA0061.10.0041
MA0062.25.44632e-21
MA0065.20.0416
MA0066.10.281
MA0067.10.803
MA0068.10.523
MA0069.10.861
MA0070.10.615
MA0071.10.61
MA0072.10.278
MA0073.10.825
MA0074.10.588
MA0076.13.49033e-10
MA0077.10.0595
MA0078.10.765
MA0079.20.457
MA0080.21.70467e-13
MA0081.10.00694
MA0083.10.0241
MA0084.10.577
MA0087.10.921
MA0088.10.0444
MA0090.11.34818e-4
MA0091.10.754
MA0092.10.985
MA0093.10.828
MA0099.20.0033
MA0100.10.352
MA0101.10.714
MA0102.20.913
MA0103.10.11
MA0104.20.127
MA0105.11.52569e-5
MA0106.10.193
MA0107.10.948
MA0108.21.01887e-10
MA0111.10.167
MA0112.20.254
MA0113.10.385
MA0114.10.24
MA0115.10.966
MA0116.14.77327e-5
MA0117.10.669
MA0119.10.578
MA0122.10.145
MA0124.10.668
MA0125.10.32
MA0131.10.334
MA0135.10.803
MA0136.11.10153e-26
MA0137.20.0127
MA0138.20.622
MA0139.10.00836
MA0140.10.161
MA0141.10.972
MA0142.10.148
MA0143.10.196
MA0144.10.14
MA0145.10.69
MA0146.10.361
MA0147.10.129
MA0148.10.27
MA0149.10.227
MA0150.10.325
MA0152.10.0208
MA0153.10.432
MA0154.10.0118
MA0155.10.739
MA0156.12.73653e-27
MA0157.10.0019
MA0159.10.15
MA0160.10.46
MA0162.10.821
MA0163.11.35021e-10
MA0164.10.451
MA0258.10.312
MA0259.10.41



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: CNhs12176

Novel motifP-value
10.234
100.0201
1000.982
1010.317
1020.71
1030.261
1040.382
1050.0738
1060.902
1070.0976
1080.708
1090.05
110.0902
1100.383
1110.45
1120.35
1130.213
1140.229
1150.204
1160.757
1170.00487
1180.405
1190.574
120.587
1200.619
1210.963
1220.258
1230.0498
1240.157
1250.943
1260.267
1270.589
1280.949
1290.534
130.541
1300.697
1310.648
1320.804
1330.577
1340.952
1350.385
1360.964
1370.137
1380.389
1390.0136
140.32
1400.0806
1410.732
1420.383
1435.59235e-5
1440.925
1450.306
1460.129
1470.0462
1480.144
1490.767
150.0768
1500.758
1510.224
1520.384
1530.751
1540.945
1550.029
1560.707
1570.307
1580.228
1590.0802
160.821
1600.743
1610.346
1620.303
1630.93
1640.249
1650.643
1660.4
1670.291
1680.192
1690.91
170.914
180.773
190.307
20.767
200.965
210.45
220.974
230.64
240.603
250.0418
260.349
270.0407
280.363
290.0754
30.0357
300.471
310.91
320.118
330.467
340.947
350.101
360.0291
370.207
380.594
390.398
40.8
400.57
410.187
420.0455
430.246
440.575
450.806
460.15
470.066
480.147
490.14
50.171
500.523
510.564
520.252
530.205
540.562
550.22
560.505
570.555
580.0497
590.479
60.881
600.382
610.0819
620.023
630.773
640.224
650.767
660.706
670.957
680.656
690.892
70.176
700.0106
710.13
720.0652
730.673
740.673
750.0145
760.185
770.415
780.0863
790.199
80.982
809.17574e-4
810.31
820.0987
830.966
840.345
850.687
860.184
870.671
880.869
890.824
90.489
900.0165
910.952
920.398
930.279
940.0938
950.0105
960.221
970.381
980.135
990.0876



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: CNhs12176


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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