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FF:11920-125H3: 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, donor3
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 number67-68
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-Basophils0.386
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0595
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-lymphoma0.18
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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-Whole0.0531
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: CNhs13812

Jaspar motifP-value
MA0002.22.34806e-5
MA0003.10.936
MA0004.10.97
MA0006.10.593
MA0007.10.754
MA0009.10.549
MA0014.10.857
MA0017.10.138
MA0018.20.271
MA0019.10.114
MA0024.10.341
MA0025.10.286
MA0027.10.708
MA0028.18.46041e-4
MA0029.10.456
MA0030.10.445
MA0031.10.593
MA0035.20.197
MA0038.10.0368
MA0039.20.972
MA0040.10.241
MA0041.10.238
MA0042.10.469
MA0043.10.335
MA0046.10.0419
MA0047.20.921
MA0048.10.969
MA0050.12.55764e-10
MA0051.10.00108
MA0052.10.00643
MA0055.10.792
MA0057.10.708
MA0058.10.881
MA0059.10.428
MA0060.10.324
MA0061.15.318e-4
MA0062.21.10955e-10
MA0065.20.0564
MA0066.10.372
MA0067.10.457
MA0068.10.383
MA0069.10.682
MA0070.10.513
MA0071.10.551
MA0072.10.534
MA0073.10.896
MA0074.10.74
MA0076.17.63918e-5
MA0077.10.0263
MA0078.10.701
MA0079.20.395
MA0080.21.75112e-10
MA0081.10.0571
MA0083.10.134
MA0084.10.934
MA0087.10.404
MA0088.10.238
MA0090.11.78624e-4
MA0091.10.971
MA0092.10.974
MA0093.10.907
MA0099.20.006
MA0100.10.901
MA0101.10.101
MA0102.20.445
MA0103.10.0451
MA0104.20.288
MA0105.14.08503e-8
MA0106.10.826
MA0107.10.257
MA0108.21.8393e-10
MA0111.10.0579
MA0112.20.105
MA0113.10.629
MA0114.10.187
MA0115.10.956
MA0116.12.48093e-6
MA0117.10.55
MA0119.10.954
MA0122.10.771
MA0124.10.274
MA0125.10.41
MA0131.10.368
MA0135.10.0419
MA0136.11.33868e-17
MA0137.20.258
MA0138.20.229
MA0139.10.0517
MA0140.10.397
MA0141.10.506
MA0142.10.416
MA0143.10.0874
MA0144.10.329
MA0145.10.705
MA0146.10.0982
MA0147.10.247
MA0148.10.586
MA0149.10.0375
MA0150.10.798
MA0152.10.0413
MA0153.10.0763
MA0154.10.023
MA0155.10.69
MA0156.16.44475e-13
MA0157.10.287
MA0159.10.228
MA0160.10.393
MA0162.10.568
MA0163.15.4441e-11
MA0164.10.838
MA0258.10.0388
MA0259.10.445



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: CNhs13812

Novel motifP-value
10.0883
100.00689
1000.441
1010.0573
1020.434
1030.49
1040.707
1050.334
1060.332
1070.664
1080.72
1090.0452
110.0284
1100.353
1110.133
1120.181
1130.312
1140.23
1150.584
1160.449
1170.00208
1180.401
1190.44
120.585
1200.43
1210.389
1220.699
1232.24352e-7
1240.234
1250.908
1260.459
1270.734
1280.597
1290.63
130.322
1300.509
1310.759
1320.881
1330.175
1340.729
1350.71
1360.662
1370.0437
1380.21
1390.153
140.276
1400.127
1410.367
1420.811
1430.0118
1440.391
1450.172
1460.706
1470.0974
1480.0421
1490.909
150.204
1500.458
1510.556
1520.606
1530.939
1540.418
1550.0446
1560.508
1570.113
1580.226
1590.671
160.609
1600.429
1610.165
1620.381
1630.54
1640.0848
1650.233
1660.857
1670.239
1680.989
1690.12
170.715
180.718
190.689
20.796
200.48
210.222
220.821
230.941
240.973
250.149
260.0357
270.368
280.519
290.0186
30.0289
300.0678
310.908
320.507
330.546
340.926
350.322
360.0163
370.156
380.598
390.622
40.844
400.199
410.675
420.0796
430.317
440.363
450.434
460.125
470.0123
480.0616
490.0937
50.828
500.774
510.644
520.51
530.143
540.751
550.756
560.461
570.21
580.119
590.489
60.338
600.379
610.135
620.0631
630.439
640.161
650.694
660.611
670.97
680.864
690.906
70.3
700.0455
710.024
720.057
730.39
740.489
750.0238
760.188
770.747
780.0527
790.793
80.501
800.295
810.321
820.0529
830.695
840.0457
850.984
860.122
870.54
880.844
890.376
90.96
900.0202
910.477
920.303
930.501
940.133
950.018
960.0798
970.224
980.119
990.059



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: CNhs13812


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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