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FF:11916-125G8: 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 17:39, 29 March 2012


Name:CD4+CD25+CD45RA- memory regulatory T cells expanded, 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 number59-60
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-Basophils0.306
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0299
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0151
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.189
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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-Whole0.0523
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: CNhs13811

Jaspar motifP-value
MA0002.22.77628e-5
MA0003.10.897
MA0004.10.848
MA0006.10.737
MA0007.10.839
MA0009.10.349
MA0014.10.944
MA0017.10.0838
MA0018.20.999
MA0019.10.103
MA0024.10.479
MA0025.10.188
MA0027.10.764
MA0028.10.0016
MA0029.10.381
MA0030.10.307
MA0031.10.833
MA0035.20.167
MA0038.10.0278
MA0039.20.941
MA0040.10.339
MA0041.10.237
MA0042.10.47
MA0043.10.131
MA0046.10.071
MA0047.20.899
MA0048.10.89
MA0050.11.8144e-7
MA0051.10.0206
MA0052.10.0095
MA0055.10.865
MA0057.10.866
MA0058.10.756
MA0059.10.373
MA0060.10.24
MA0061.10.00829
MA0062.24.39736e-10
MA0065.20.0296
MA0066.10.295
MA0067.10.578
MA0068.10.385
MA0069.10.683
MA0070.10.46
MA0071.10.464
MA0072.10.691
MA0073.10.832
MA0074.10.864
MA0076.11.83922e-4
MA0077.10.0659
MA0078.10.704
MA0079.20.419
MA0080.25.21874e-10
MA0081.10.0795
MA0083.10.132
MA0084.10.803
MA0087.10.379
MA0088.10.164
MA0090.12.48428e-4
MA0091.10.868
MA0092.10.709
MA0093.10.945
MA0099.27.87188e-4
MA0100.10.854
MA0101.10.544
MA0102.20.255
MA0103.10.0271
MA0104.20.286
MA0105.14.59636e-7
MA0106.10.636
MA0107.10.961
MA0108.22.99292e-11
MA0111.10.0489
MA0112.20.0785
MA0113.10.703
MA0114.10.148
MA0115.10.463
MA0116.11.96678e-6
MA0117.10.801
MA0119.10.903
MA0122.10.94
MA0124.10.37
MA0125.10.364
MA0131.10.457
MA0135.10.0872
MA0136.16.81159e-17
MA0137.20.391
MA0138.20.213
MA0139.10.0246
MA0140.10.386
MA0141.10.443
MA0142.10.629
MA0143.10.168
MA0144.10.383
MA0145.10.861
MA0146.10.0714
MA0147.10.255
MA0148.10.479
MA0149.10.0341
MA0150.10.892
MA0152.10.0386
MA0153.10.0702
MA0154.10.0132
MA0155.10.856
MA0156.11.10357e-11
MA0157.10.413
MA0159.10.227
MA0160.10.419
MA0162.10.518
MA0163.11.36512e-11
MA0164.10.821
MA0258.10.0253
MA0259.10.45



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: CNhs13811

Novel motifP-value
10.0806
100.00715
1000.414
1010.0875
1020.455
1030.53
1040.807
1050.333
1060.223
1070.936
1080.864
1090.0359
110.0183
1100.37
1110.147
1120.111
1130.43
1140.113
1150.616
1160.316
1170.0023
1180.438
1190.316
120.601
1200.258
1210.563
1220.778
1231.69696e-6
1240.183
1250.954
1260.633
1270.411
1280.564
1290.331
130.308
1300.649
1310.811
1320.774
1330.131
1340.69
1350.651
1360.692
1370.0832
1380.218
1390.125
140.274
1400.127
1410.451
1420.7
1430.0109
1440.417
1450.121
1460.771
1470.105
1480.0262
1490.888
150.233
1500.506
1510.486
1520.716
1530.808
1540.473
1550.0361
1560.616
1570.186
1580.192
1590.77
160.506
1600.359
1610.0763
1620.327
1630.337
1640.0694
1650.312
1660.84
1670.228
1680.98
1690.108
170.692
180.554
190.751
20.992
200.594
210.166
220.866
230.955
240.857
250.183
260.0349
270.317
280.561
290.026
30.0267
300.0913
310.983
320.704
330.561
340.944
350.28
360.0141
370.139
380.526
390.759
40.917
400.217
410.692
420.0865
430.276
440.23
450.481
460.0588
470.00938
480.0324
490.0871
50.85
500.795
510.667
520.56
530.168
540.705
550.781
560.441
570.136
580.17
590.372
60.419
600.356
610.122
620.0844
630.36
640.14
650.547
660.779
670.949
680.958
690.798
70.327
700.0312
710.0347
720.0742
730.321
740.555
750.0258
760.279
770.964
780.044
790.939
80.342
800.304
810.245
820.05
830.56
840.0484
850.91
860.129
870.513
880.849
890.501
90.957
900.0601
910.36
920.363
930.459
940.17
950.013
960.0508
970.232
980.134
990.17



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: CNhs13811


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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