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FF:12201-129C5: 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, 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
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-0.256
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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-Whole0.86
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: CNhs12182

Jaspar motifP-value
MA0002.23.12275e-10
MA0003.10.377
MA0004.10.988
MA0006.10.578
MA0007.10.997
MA0009.10.249
MA0014.10.644
MA0017.10.0259
MA0018.20.356
MA0019.10.866
MA0024.10.122
MA0025.10.689
MA0027.10.723
MA0028.10.0234
MA0029.10.987
MA0030.10.366
MA0031.10.0281
MA0035.20.107
MA0038.10.116
MA0039.20.836
MA0040.10.677
MA0041.10.607
MA0042.10.553
MA0043.10.251
MA0046.10.94
MA0047.20.0679
MA0048.10.248
MA0050.11.85035e-6
MA0051.10.00414
MA0052.10.00741
MA0055.10.318
MA0057.10.796
MA0058.10.906
MA0059.10.321
MA0060.10.0214
MA0061.10.00389
MA0062.21.44118e-9
MA0065.20.0178
MA0066.10.0934
MA0067.10.87
MA0068.10.825
MA0069.10.66
MA0070.10.396
MA0071.10.481
MA0072.10.324
MA0073.10.866
MA0074.10.714
MA0076.10.00205
MA0077.10.168
MA0078.10.809
MA0079.20.272
MA0080.21.99224e-14
MA0081.10.00848
MA0083.10.15
MA0084.10.802
MA0087.10.926
MA0088.10.0739
MA0090.10.00423
MA0091.10.655
MA0092.10.569
MA0093.10.879
MA0099.20.785
MA0100.10.732
MA0101.10.524
MA0102.20.559
MA0103.10.129
MA0104.20.212
MA0105.17.30713e-7
MA0106.10.788
MA0107.10.477
MA0108.27.05723e-9
MA0111.10.245
MA0112.20.0307
MA0113.10.56
MA0114.10.118
MA0115.10.941
MA0116.18.39917e-6
MA0117.10.731
MA0119.10.54
MA0122.10.268
MA0124.10.741
MA0125.10.309
MA0131.10.789
MA0135.10.612
MA0136.17.66885e-23
MA0137.20.05
MA0138.20.84
MA0139.10.0209
MA0140.10.03
MA0141.10.566
MA0142.10.9
MA0143.10.626
MA0144.10.132
MA0145.10.633
MA0146.10.338
MA0147.10.193
MA0148.10.164
MA0149.10.2
MA0150.10.807
MA0152.10.077
MA0153.10.807
MA0154.10.00107
MA0155.10.975
MA0156.13.53298e-19
MA0157.10.0146
MA0159.10.0687
MA0160.10.307
MA0162.10.66
MA0163.13.46983e-14
MA0164.10.531
MA0258.10.0561
MA0259.10.504



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: CNhs12182

Novel motifP-value
10.17
100.03
1000.917
1010.247
1020.88
1030.271
1040.385
1050.0699
1060.32
1070.876
1080.84
1090.102
110.0629
1100.411
1110.225
1120.148
1130.147
1140.0899
1150.136
1160.982
1170.0206
1180.436
1190.297
120.942
1200.311
1210.783
1220.371
1230.082
1240.0648
1250.984
1260.16
1270.3
1280.342
1290.469
130.638
1300.853
1310.614
1320.932
1330.681
1340.757
1350.125
1360.611
1370.0957
1380.3
1390.00591
140.333
1400.0961
1410.625
1420.804
1432.42703e-5
1440.826
1450.318
1460.0996
1470.0659
1480.0535
1490.54
150.0508
1500.646
1510.203
1520.626
1530.884
1540.894
1550.0777
1560.528
1570.593
1580.186
1590.223
160.575
1600.458
1610.34
1620.394
1630.824
1640.476
1650.201
1660.689
1670.326
1680.112
1690.353
170.483
180.395
190.915
20.492
200.547
210.345
220.743
230.521
240.471
250.0736
260.384
270.0492
280.549
290.212
30.0498
300.719
310.746
320.252
330.421
340.727
350.0561
360.0137
370.213
380.525
390.772
40.766
400.466
410.113
420.0674
430.176
440.527
450.911
460.0667
470.108
480.162
490.0972
50.113
500.691
510.515
520.637
530.159
540.449
550.167
560.543
570.454
580.0353
590.247
60.773
600.244
610.177
620.0125
630.497
640.192
650.473
660.924
670.897
680.81
690.784
70.146
700.0144
710.0621
720.129
730.68
740.241
750.0493
760.432
770.98
780.17
790.351
80.525
800.00737
810.282
820.0483
830.732
840.408
850.634
860.28
870.938
880.88
890.864
90.321
900.0278
910.621
920.121
930.153
940.0488
950.0468
960.0841
970.463
980.177
990.323



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: CNhs12182


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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