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FF:11795-124C4: 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 conventional 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 number19
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-Basophils0.103
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.129
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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
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: CNhs13205

Jaspar motifP-value
MA0002.22.24458e-4
MA0003.10.421
MA0004.10.814
MA0006.10.0933
MA0007.10.91
MA0009.10.471
MA0014.10.489
MA0017.10.931
MA0018.21.24079e-5
MA0019.10.635
MA0024.10.476
MA0025.10.955
MA0027.10.798
MA0028.17.94075e-6
MA0029.10.367
MA0030.10.0303
MA0031.14.16603e-4
MA0035.20.291
MA0038.10.0676
MA0039.20.739
MA0040.10.384
MA0041.10.304
MA0042.10.835
MA0043.10.242
MA0046.10.428
MA0047.20.132
MA0048.10.724
MA0050.12.38699e-4
MA0051.10.0147
MA0052.10.00756
MA0055.10.909
MA0057.10.55
MA0058.10.836
MA0059.10.667
MA0060.10.182
MA0061.10.434
MA0062.21.88808e-17
MA0065.20.354
MA0066.10.877
MA0067.10.189
MA0068.10.939
MA0069.10.9
MA0070.10.562
MA0071.10.886
MA0072.10.644
MA0073.10.943
MA0074.10.353
MA0076.15.66826e-9
MA0077.10.0515
MA0078.10.736
MA0079.20.409
MA0080.21.82871e-9
MA0081.10.0167
MA0083.10.00164
MA0084.10.208
MA0087.10.714
MA0088.10.118
MA0090.15.05082e-4
MA0091.10.547
MA0092.10.712
MA0093.10.952
MA0099.21.56356e-9
MA0100.10.596
MA0101.10.225
MA0102.20.482
MA0103.10.138
MA0104.20.065
MA0105.10.00943
MA0106.10.14
MA0107.10.124
MA0108.21.21024e-12
MA0111.10.169
MA0112.20.746
MA0113.10.656
MA0114.10.999
MA0115.10.859
MA0116.10.00546
MA0117.10.225
MA0119.10.721
MA0122.10.478
MA0124.10.581
MA0125.10.128
MA0131.10.0575
MA0135.10.183
MA0136.17.79893e-21
MA0137.20.831
MA0138.20.212
MA0139.10.1
MA0140.10.252
MA0141.10.302
MA0142.10.0902
MA0143.10.181
MA0144.10.597
MA0145.10.0446
MA0146.10.69
MA0147.10.0838
MA0148.10.383
MA0149.10.188
MA0150.10.0294
MA0152.10.00584
MA0153.10.612
MA0154.10.42
MA0155.10.297
MA0156.11.93967e-19
MA0157.13.38371e-4
MA0159.10.541
MA0160.10.515
MA0162.10.308
MA0163.14.20868e-6
MA0164.10.942
MA0258.10.766
MA0259.10.118



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: CNhs13205

Novel motifP-value
10.432
100.0133
1000.478
1010.172
1020.896
1030.701
1040.941
1050.568
1060.826
1070.00296
1080.4
1090.311
110.3
1100.947
1110.528
1120.85
1130.427
1140.507
1150.112
1160.331
1170.002
1180.281
1190.233
120.708
1200.873
1210.848
1220.936
1234.11276e-5
1240.403
1250.78
1260.801
1270.84
1280.535
1290.556
130.644
1300.366
1310.287
1320.568
1330.533
1340.411
1350.923
1360.729
1370.0711
1380.304
1390.061
140.653
1400.158
1410.463
1420.278
1430.026
1440.753
1450.841
1460.675
1470.011
1480.468
1490.369
150.288
1500.945
1510.623
1520.16
1530.791
1540.303
1550.0271
1560.909
1570.324
1580.0191
1590.448
160.418
1600.414
1610.591
1620.174
1630.481
1640.0935
1650.657
1660.481
1670.0537
1680.939
1690.188
170.495
180.632
190.0686
20.345
200.426
210.533
220.348
230.207
240.636
250.0986
260.849
270.548
280.621
290.0221
30.143
300.0929
310.662
320.0214
330.218
340.321
350.139
360.0237
370.355
380.854
390.207
40.771
400.852
410.249
420.124
430.576
440.999
450.244
460.514
470.158
480.377
490.13
50.476
500.43
510.908
520.22
530.492
540.967
550.522
560.992
570.561
580.17
590.437
60.76
600.949
610.0721
620.2
630.916
640.587
650.558
660.64
670.74
680.414
690.986
70.462
700.035
710.147
720.173
730.715
740.593
750.0114
760.0721
770.0235
780.668
790.583
80.806
800.0325
810.314
820.251
830.766
840.618
850.377
860.314
870.648
880.942
890.0532
90.702
900.0267
910.621
920.897
930.72
940.294
950.3
960.391
970.358
980.199
990.00114



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: CNhs13205


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)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000810 (CD4-positive, alpha-beta thymocyte)
0000813 (memory T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)
0000896 (activated CD4-positive, alpha-beta T cell)
0000897 (CD4-positive, alpha-beta memory T 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)
0002425 (early T lineage precursor)
0002427 (resting double-positive thymocyte)
0002428 (double-positive blast)
0002429 (CD69-positive double-positive thymocyte)
0002431 (CD4-positive, CD8-intermediate double-positive thymocyte)
0002432 (CD24-positive, CD4 single-positive thymocyte)
0002433 (CD69-positive, CD4-positive single-positive thymocyte)
0002436 (mature CD4 single-positive thymocyte)
0002489 (double negative thymocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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