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FF:11797-124C6: 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 17:30, 29 March 2012


Name:CD4+CD25+CD45RA- memory regulatory T cells, donor2
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
sexmale
age23
cell typeT cell
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number23
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-Basophils0.974
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-0.157
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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-Whole0.0869
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: CNhs13206

Jaspar motifP-value
MA0002.22.29387e-6
MA0003.10.878
MA0004.10.836
MA0006.10.262
MA0007.10.896
MA0009.10.15
MA0014.10.888
MA0017.10.32
MA0018.21.19082e-5
MA0019.10.928
MA0024.10.655
MA0025.10.368
MA0027.10.874
MA0028.16.5754e-5
MA0029.10.266
MA0030.10.0146
MA0031.15.38778e-4
MA0035.20.0675
MA0038.10.103
MA0039.20.921
MA0040.10.953
MA0041.10.383
MA0042.10.892
MA0043.10.14
MA0046.10.232
MA0047.20.0707
MA0048.10.746
MA0050.13.74452e-8
MA0051.10.00277
MA0052.10.00466
MA0055.10.942
MA0057.10.669
MA0058.10.705
MA0059.10.556
MA0060.10.16
MA0061.10.0112
MA0062.24.69354e-15
MA0065.20.132
MA0066.10.241
MA0067.10.0239
MA0068.10.719
MA0069.10.72
MA0070.10.641
MA0071.10.591
MA0072.10.0724
MA0073.10.904
MA0074.10.429
MA0076.15.9273e-7
MA0077.10.0273
MA0078.10.655
MA0079.20.353
MA0080.24.29838e-11
MA0081.10.0206
MA0083.10.04
MA0084.10.401
MA0087.10.563
MA0088.10.279
MA0090.11.43113e-4
MA0091.10.934
MA0092.10.978
MA0093.10.946
MA0099.20.00646
MA0100.10.556
MA0101.10.694
MA0102.20.538
MA0103.10.112
MA0104.20.238
MA0105.12.37556e-6
MA0106.10.209
MA0107.10.962
MA0108.21.03349e-8
MA0111.10.169
MA0112.20.298
MA0113.10.801
MA0114.10.53
MA0115.10.619
MA0116.11.69905e-4
MA0117.10.114
MA0119.10.536
MA0122.10.578
MA0124.10.401
MA0125.10.172
MA0131.10.17
MA0135.10.414
MA0136.18.09804e-22
MA0137.20.842
MA0138.20.317
MA0139.10.027
MA0140.10.0532
MA0141.10.76
MA0142.10.263
MA0143.10.493
MA0144.10.981
MA0145.10.308
MA0146.10.638
MA0147.10.207
MA0148.10.363
MA0149.10.0899
MA0150.10.975
MA0152.10.0135
MA0153.10.119
MA0154.10.0378
MA0155.10.364
MA0156.11.09838e-16
MA0157.15.76995e-4
MA0159.10.295
MA0160.10.748
MA0162.10.933
MA0163.11.12192e-7
MA0164.10.466
MA0258.10.275
MA0259.10.316



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: CNhs13206

Novel motifP-value
10.279
100.0112
1000.684
1010.203
1020.746
1030.328
1040.813
1050.286
1060.344
1070.0422
1080.677
1090.0818
110.0892
1100.683
1110.637
1120.477
1130.358
1140.259
1150.44
1160.548
1170.00275
1180.284
1190.713
120.842
1200.588
1210.822
1220.706
1230.0015
1240.293
1250.835
1260.553
1270.807
1280.99
1290.794
130.511
1300.372
1310.861
1320.284
1330.992
1340.9
1350.885
1360.8
1370.0594
1380.313
1390.0908
140.484
1400.124
1410.439
1420.535
1430.00171
1440.927
1450.605
1460.413
1470.0576
1480.0485
1490.69
150.107
1500.637
1510.596
1520.555
1530.751
1540.477
1550.00679
1560.49
1570.186
1580.0437
1590.17
160.836
1600.697
1610.896
1620.0289
1630.625
1640.0533
1650.586
1660.461
1670.161
1680.752
1690.852
170.938
180.806
190.228
20.639
200.456
210.672
220.584
230.552
240.765
250.056
260.312
270.42
280.582
290.00597
30.112
300.122
310.808
320.263
330.192
340.423
350.19
360.0273
370.18
380.918
390.41
40.94
400.534
410.175
420.116
430.333
440.505
450.354
460.26
470.0947
480.229
490.114
50.357
500.427
510.709
520.394
530.47
540.924
550.742
560.86
570.514
580.0934
590.892
60.987
600.398
610.0991
620.0823
630.899
640.406
650.953
660.792
670.775
680.642
690.643
70.214
700.0179
710.0469
720.0406
730.55
740.622
750.0188
760.154
770.105
780.171
790.685
80.967
800.0194
810.373
820.0923
830.541
840.462
850.897
860.103
870.825
880.938
890.139
90.931
900.0358
910.686
920.387
930.815
940.0998
950.0198
960.224
970.296
980.0844
994.02007e-4



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: CNhs13206


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)
0000624 (CD4-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)
0000792 (CD4-positive, CD25-positive, alpha-beta regulatory T cell)
0000815 (regulatory T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000898 (naive T 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)
0002677 (naive regulatory 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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