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FF:12211-129D6: 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, donation3
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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.14
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-0.233
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-Whole0.924
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: CNhs12187

Jaspar motifP-value
MA0002.28.27544e-10
MA0003.10.776
MA0004.10.894
MA0006.10.406
MA0007.10.679
MA0009.10.356
MA0014.10.901
MA0017.10.0177
MA0018.20.669
MA0019.10.483
MA0024.10.149
MA0025.10.453
MA0027.10.695
MA0028.11.69268e-4
MA0029.10.708
MA0030.10.11
MA0031.10.00923
MA0035.20.0694
MA0038.10.0742
MA0039.20.789
MA0040.10.687
MA0041.10.44
MA0042.10.47
MA0043.10.14
MA0046.10.783
MA0047.20.0873
MA0048.10.444
MA0050.14.25609e-8
MA0051.12.44114e-4
MA0052.10.0275
MA0055.10.452
MA0057.10.755
MA0058.10.691
MA0059.10.268
MA0060.10.125
MA0061.10.00774
MA0062.27.15354e-17
MA0065.20.0197
MA0066.10.118
MA0067.10.889
MA0068.10.966
MA0069.10.893
MA0070.10.519
MA0071.10.494
MA0072.10.441
MA0073.10.834
MA0074.10.986
MA0076.11.90175e-7
MA0077.10.116
MA0078.10.639
MA0079.20.33
MA0080.22.93449e-13
MA0081.10.00639
MA0083.10.0658
MA0084.10.647
MA0087.10.882
MA0088.10.0555
MA0090.16.8192e-4
MA0091.10.718
MA0092.10.828
MA0093.10.973
MA0099.20.216
MA0100.10.524
MA0101.10.757
MA0102.20.779
MA0103.10.127
MA0104.20.195
MA0105.18.85378e-6
MA0106.10.179
MA0107.10.895
MA0108.21.85631e-9
MA0111.10.176
MA0112.20.132
MA0113.10.543
MA0114.10.114
MA0115.10.909
MA0116.12.82452e-5
MA0117.10.725
MA0119.10.837
MA0122.10.132
MA0124.10.617
MA0125.10.778
MA0131.10.517
MA0135.10.843
MA0136.13.38042e-24
MA0137.20.11
MA0138.20.937
MA0139.10.00886
MA0140.10.0651
MA0141.10.74
MA0142.10.638
MA0143.10.58
MA0144.10.281
MA0145.10.972
MA0146.10.427
MA0147.10.182
MA0148.10.122
MA0149.10.0946
MA0150.10.66
MA0152.10.0936
MA0153.10.596
MA0154.10.00677
MA0155.10.705
MA0156.13.45293e-22
MA0157.10.0111
MA0159.10.105
MA0160.10.341
MA0162.10.882
MA0163.11.2789e-11
MA0164.10.518
MA0258.10.199
MA0259.10.481



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: CNhs12187

Novel motifP-value
10.239
100.0174
1000.9
1010.251
1020.514
1030.157
1040.435
1050.18
1060.643
1070.231
1080.676
1090.0478
110.0574
1100.519
1110.286
1120.373
1130.275
1140.187
1150.127
1160.745
1170.00463
1180.298
1190.807
120.688
1200.499
1210.781
1220.253
1230.111
1240.0597
1250.853
1260.258
1270.406
1280.782
1290.243
130.601
1300.593
1310.725
1320.747
1330.983
1340.881
1350.253
1360.775
1370.0599
1380.343
1390.0069
140.256
1400.0363
1410.988
1420.932
1432.42916e-5
1440.702
1450.426
1460.145
1470.0414
1480.228
1490.644
150.0508
1500.754
1510.348
1520.42
1530.73
1540.973
1550.0411
1560.446
1570.645
1580.142
1590.125
160.702
1600.778
1610.376
1620.265
1630.834
1640.398
1650.301
1660.621
1670.284
1680.0885
1690.782
170.626
180.439
190.57
20.594
200.855
210.44
220.856
230.851
240.55
250.0748
260.425
270.0231
280.323
290.0391
30.054
300.643
310.529
320.312
330.507
340.682
350.0526
360.0213
370.164
380.542
390.627
40.638
400.488
410.116
420.0591
430.202
440.582
450.998
460.0918
470.0631
480.132
490.113
50.152
500.58
510.525
520.439
530.222
540.422
550.319
560.54
570.623
580.0467
590.339
60.891
600.282
610.0857
620.022
630.698
640.176
650.585
660.709
670.838
680.786
690.807
70.164
700.0123
710.0764
720.0305
730.651
740.392
750.0247
760.378
770.615
780.122
790.333
80.772
808.81702e-4
810.338
820.0955
830.667
840.556
850.714
860.151
870.626
880.823
890.783
90.403
900.0779
910.881
920.239
930.155
940.0696
950.0217
960.0816
970.44
980.271
990.102



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: CNhs12187


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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