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FF:11226-116C2: 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 16:34, 29 March 2012


Name:CD8+ T Cells, donor1
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 stage47 years old adult
sexmale
age47
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 numberCD8T725
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-Basophils0.257
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.118
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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-Whole0.751
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: CNhs10854

Jaspar motifP-value
MA0002.24.78047e-5
MA0003.10.369
MA0004.10.896
MA0006.10.213
MA0007.10.216
MA0009.10.0143
MA0014.10.721
MA0017.10.0621
MA0018.24.7314e-11
MA0019.10.688
MA0024.10.746
MA0025.10.0505
MA0027.10.718
MA0028.10.0019
MA0029.10.939
MA0030.18.66694e-4
MA0031.13.75933e-6
MA0035.20.194
MA0038.10.114
MA0039.20.387
MA0040.10.799
MA0041.10.242
MA0042.10.655
MA0043.13.67435e-5
MA0046.10.0986
MA0047.20.264
MA0048.10.866
MA0050.13.65412e-8
MA0051.10.00216
MA0052.10.0218
MA0055.10.736
MA0057.10.165
MA0058.10.935
MA0059.10.65
MA0060.10.52
MA0061.13.59376e-10
MA0062.25.25739e-15
MA0065.20.507
MA0066.10.755
MA0067.10.00137
MA0068.10.872
MA0069.10.98
MA0070.10.521
MA0071.10.948
MA0072.10.00236
MA0073.10.516
MA0074.10.554
MA0076.14.02483e-4
MA0077.10.162
MA0078.10.995
MA0079.20.975
MA0080.22.47901e-10
MA0081.10.00642
MA0083.10.266
MA0084.10.2
MA0087.10.604
MA0088.10.307
MA0090.11.34006e-4
MA0091.10.251
MA0092.10.757
MA0093.10.822
MA0099.20.991
MA0100.10.625
MA0101.14.79375e-7
MA0102.20.422
MA0103.10.69
MA0104.20.547
MA0105.19.23314e-7
MA0106.10.0276
MA0107.15.04468e-7
MA0108.28.84494e-4
MA0111.10.58
MA0112.20.0514
MA0113.10.307
MA0114.10.114
MA0115.10.147
MA0116.10.367
MA0117.10.00611
MA0119.10.188
MA0122.10.997
MA0124.10.177
MA0125.10.115
MA0131.10.051
MA0135.10.182
MA0136.11.83799e-18
MA0137.20.28
MA0138.20.0146
MA0139.10.645
MA0140.10.339
MA0141.10.0462
MA0142.10.184
MA0143.10.155
MA0144.10.405
MA0145.10.0201
MA0146.10.863
MA0147.10.54
MA0148.10.471
MA0149.10.833
MA0150.10.315
MA0152.10.00269
MA0153.10.109
MA0154.10.699
MA0155.10.135
MA0156.18.40116e-14
MA0157.16.82279e-4
MA0159.10.905
MA0160.10.524
MA0162.10.195
MA0163.10.0508
MA0164.10.848
MA0258.10.354
MA0259.10.623



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: CNhs10854

Novel motifP-value
10.817
100.0236
1000.931
1010.445
1020.945
1030.328
1040.839
1050.606
1060.377
1070.0142
1080.432
1090.978
110.984
1100.188
1110.715
1120.726
1130.314
1140.868
1150.284
1160.112
1170.0162
1180.644
1190.197
120.57
1200.262
1210.681
1220.866
1238.73851e-4
1240.788
1250.432
1260.826
1270.658
1280.765
1290.171
130.625
1300.317
1310.219
1320.137
1330.943
1340.662
1350.344
1360.933
1370.0643
1380.727
1390.197
140.575
1400.946
1410.687
1420.356
1430.0188
1440.864
1450.462
1460.467
1470.0165
1480.474
1490.108
150.456
1500.975
1510.701
1520.725
1530.539
1540.182
1550.0613
1560.999
1570.571
1580.00776
1590.764
160.172
1600.0144
1610.73
1620.00913
1630.879
1640.17
1650.811
1660.276
1670.172
1680.578
1690.0833
170.507
180.599
190.0163
20.147
200.152
210.711
220.162
230.528
240.557
250.217
260.651
270.497
280.361
290.11
30.828
300.0643
310.534
320.00255
330.411
340.311
350.486
360.137
370.52
380.496
390.38
40.634
400.772
410.13
420.437
430.818
440.596
450.127
460.773
470.875
480.802
490.382
50.725
500.476
510.843
520.774
530.381
540.84
550.524
560.716
570.683
580.244
590.144
60.852
600.738
610.289
620.437
630.649
640.86
650.334
660.68
670.397
680.716
690.732
70.837
700.398
710.468
720.46
730.716
740.764
750.0859
760.179
770.00134
780.93
790.95
80.197
800.0248
810.755
820.849
830.769
840.204
850.89
860.0743
870.993
880.894
890.00213
90.733
900.936
910.918
920.695
930.983
940.392
950.28
960.866
970.311
980.775
991.38602e-6



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: CNhs10854


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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