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FF:11794-124C3: 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 expanded, 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 stageNA
sexmale
age25
cell typeT cell
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number17
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-Basophils0.408
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-lymphoma0.216
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-Whole0.0874
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: CNhs13204

Jaspar motifP-value
MA0002.23.27919e-9
MA0003.10.507
MA0004.10.671
MA0006.10.704
MA0007.10.526
MA0009.10.182
MA0014.10.97
MA0017.10.0397
MA0018.20.252
MA0019.10.96
MA0024.10.726
MA0025.10.243
MA0027.10.935
MA0028.14.391e-5
MA0029.10.409
MA0030.10.869
MA0031.10.313
MA0035.20.0252
MA0038.10.0543
MA0039.20.967
MA0040.10.552
MA0041.10.741
MA0042.10.885
MA0043.10.387
MA0046.10.144
MA0047.20.389
MA0048.10.643
MA0050.12.73589e-8
MA0051.10.00357
MA0052.10.00109
MA0055.10.625
MA0057.10.852
MA0058.10.958
MA0059.10.518
MA0060.10.528
MA0061.16.84243e-4
MA0062.21.93075e-15
MA0065.20.0232
MA0066.10.218
MA0067.10.424
MA0068.10.154
MA0069.10.364
MA0070.10.776
MA0071.10.431
MA0072.10.328
MA0073.10.712
MA0074.10.968
MA0076.16.38725e-8
MA0077.10.0131
MA0078.10.911
MA0079.20.568
MA0080.22.17815e-13
MA0081.10.0148
MA0083.10.31
MA0084.10.933
MA0087.10.464
MA0088.10.126
MA0090.19.26151e-5
MA0091.10.751
MA0092.10.686
MA0093.10.697
MA0099.20.103
MA0100.10.246
MA0101.10.121
MA0102.20.702
MA0103.10.0833
MA0104.20.394
MA0105.11.26667e-7
MA0106.10.891
MA0107.10.212
MA0108.22.12172e-10
MA0111.10.0619
MA0112.20.0625
MA0113.10.553
MA0114.10.139
MA0115.10.71
MA0116.13.96116e-6
MA0117.10.511
MA0119.10.378
MA0122.10.872
MA0124.10.554
MA0125.10.655
MA0131.10.468
MA0135.10.195
MA0136.18.74158e-26
MA0137.20.0167
MA0138.20.475
MA0139.10.00691
MA0140.10.0393
MA0141.10.568
MA0142.10.503
MA0143.10.179
MA0144.10.0786
MA0145.10.803
MA0146.10.263
MA0147.10.363
MA0148.10.87
MA0149.10.131
MA0150.10.869
MA0152.10.0378
MA0153.10.275
MA0154.10.00616
MA0155.10.877
MA0156.16.92387e-24
MA0157.10.108
MA0159.10.105
MA0160.10.24
MA0162.10.533
MA0163.14.28765e-12
MA0164.10.612
MA0258.10.0705
MA0259.10.587



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: CNhs13204

Novel motifP-value
10.131
100.0149
1000.811
1010.22
1020.575
1030.0787
1040.673
1050.14
1060.349
1070.399
1080.663
1090.0409
110.027
1100.456
1110.279
1120.0682
1130.575
1140.102
1150.341
1160.789
1170.00275
1180.372
1190.715
120.439
1200.205
1210.4
1220.21
1230.0118
1240.14
1250.783
1260.208
1270.362
1280.725
1290.329
130.487
1300.88
1310.805
1320.821
1330.35
1340.843
1350.638
1360.591
1370.0237
1380.146
1390.112
140.309
1400.0705
1410.478
1420.941
1432.59906e-4
1440.419
1450.261
1460.58
1470.0346
1480.0462
1490.804
150.086
1500.452
1510.649
1520.717
1530.883
1540.789
1550.029
1560.608
1570.0683
1580.431
1590.273
160.475
1600.558
1610.229
1620.0848
1630.536
1640.145
1650.244
1660.659
1670.562
1680.258
1690.22
170.826
180.383
190.779
20.911
200.742
210.461
220.965
230.803
240.729
250.0701
260.114
270.14
280.426
290.00715
30.0381
300.224
310.996
320.55
330.411
340.951
350.194
360.0212
370.129
380.648
390.409
40.961
400.293
410.355
420.0631
430.34
440.228
450.667
460.0771
470.00567
480.0393
490.209
50.448
500.66
510.527
520.332
530.468
540.8
550.73
560.484
570.43
580.094
590.171
60.739
600.385
610.0999
620.0364
630.645
640.159
650.816
660.952
670.71
680.762
690.798
70.244
700.0265
710.0191
720.016
730.359
740.297
750.0185
760.412
770.721
780.0492
790.488
80.544
800.0271
810.352
820.0548
830.912
840.264
850.731
860.13
870.191
880.683
890.931
90.586
900.034
910.562
920.388
930.29
940.0985
950.0146
960.0351
970.324
980.35
990.0399



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: CNhs13204


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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