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FF:11793-124C2: 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+ naive 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 number15
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-Basophils0.264
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.144
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-0.0195
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
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: CNhs13203

Jaspar motifP-value
MA0002.28.89312e-7
MA0003.10.449
MA0004.10.737
MA0006.10.458
MA0007.10.661
MA0009.10.619
MA0014.10.978
MA0017.10.0146
MA0018.20.763
MA0019.10.913
MA0024.10.958
MA0025.10.184
MA0027.10.874
MA0028.13.75382e-6
MA0029.10.593
MA0030.10.754
MA0031.10.156
MA0035.20.0662
MA0038.10.0511
MA0039.20.923
MA0040.10.327
MA0041.10.994
MA0042.10.957
MA0043.10.0864
MA0046.10.235
MA0047.20.409
MA0048.10.466
MA0050.18.79187e-6
MA0051.10.0125
MA0052.12.34547e-4
MA0055.10.879
MA0057.10.92
MA0058.10.548
MA0059.10.319
MA0060.10.231
MA0061.10.0227
MA0062.26.76958e-17
MA0065.20.0108
MA0066.10.237
MA0067.10.63
MA0068.10.0761
MA0069.10.778
MA0070.10.626
MA0071.10.382
MA0072.10.757
MA0073.10.88
MA0074.10.41
MA0076.12.25671e-9
MA0077.10.0557
MA0078.10.736
MA0079.20.48
MA0080.23.29939e-12
MA0081.10.0217
MA0083.10.00674
MA0084.10.823
MA0087.10.376
MA0088.10.0489
MA0090.16.10528e-5
MA0091.10.521
MA0092.10.529
MA0093.10.802
MA0099.20.00344
MA0100.10.476
MA0101.10.819
MA0102.20.329
MA0103.10.0134
MA0104.20.1
MA0105.14.87997e-6
MA0106.10.521
MA0107.10.781
MA0108.21.60731e-16
MA0111.10.0605
MA0112.20.0459
MA0113.10.821
MA0114.10.101
MA0115.10.521
MA0116.11.25873e-5
MA0117.10.642
MA0119.10.558
MA0122.10.643
MA0124.10.978
MA0125.10.392
MA0131.10.564
MA0135.10.125
MA0136.12.23841e-24
MA0137.20.00145
MA0138.20.588
MA0139.10.00947
MA0140.10.106
MA0141.10.335
MA0142.10.765
MA0143.10.393
MA0144.10.0772
MA0145.10.969
MA0146.10.293
MA0147.10.0826
MA0148.10.911
MA0149.10.0652
MA0150.10.514
MA0152.10.00441
MA0153.10.352
MA0154.10.00639
MA0155.10.91
MA0156.11.13269e-19
MA0157.10.0173
MA0159.10.136
MA0160.10.125
MA0162.10.717
MA0163.12.67812e-12
MA0164.10.674
MA0258.10.0524
MA0259.10.301



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: CNhs13203

Novel motifP-value
10.106
100.0225
1000.859
1010.126
1020.599
1030.0278
1040.596
1050.178
1060.654
1070.422
1080.803
1090.0286
110.0293
1100.402
1110.213
1120.0973
1130.757
1140.0586
1150.142
1160.781
1170.00196
1180.332
1190.587
120.467
1200.0512
1210.882
1220.17
1230.0327
1240.0321
1250.611
1260.313
1270.246
1280.916
1290.238
130.414
1300.909
1310.784
1320.927
1330.0452
1340.401
1350.862
1360.936
1370.0717
1380.197
1390.0546
140.396
1400.0511
1410.417
1420.814
1430.00409
1440.715
1450.265
1460.355
1470.0371
1480.044
1490.755
150.086
1500.671
1510.486
1520.615
1530.993
1540.898
1550.00811
1560.396
1570.0617
1580.19
1590.287
160.353
1600.334
1610.126
1620.162
1630.719
1640.139
1650.326
1660.547
1670.208
1680.341
1690.344
170.83
180.337
190.734
20.875
200.894
210.351
220.797
230.852
240.649
250.116
260.282
270.0901
280.531
290.0121
30.0372
300.315
310.809
320.674
330.303
340.93
350.185
360.0176
370.134
380.397
390.368
40.775
400.335
410.174
420.0981
430.304
440.206
450.771
460.0511
470.00637
480.0509
490.156
50.495
500.65
510.466
520.323
530.478
540.553
550.783
560.487
570.317
580.0817
590.2
60.883
600.424
610.0727
620.0388
630.538
640.163
650.622
660.807
670.714
680.525
690.969
70.227
700.0289
710.0412
720.014
730.509
740.308
750.0124
760.349
770.836
780.0207
790.165
80.547
800.0511
810.408
820.0449
830.751
840.255
850.91
860.147
870.346
880.804
890.974
90.568
900.0224
910.521
920.268
930.127
940.111
950.0208
960.0279
970.319
980.0807
990.069



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: CNhs13203


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)
0000813 (memory T cell)
0000815 (regulatory 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)
0002678 (memory 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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