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FF:11798-124C7: 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 17:31, 29 March 2012


Name:CD4+CD25-CD45RA- memory 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 number25
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-Basophils0.612
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
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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-Whole0.376
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: CNhs13237

Jaspar motifP-value
MA0002.21.0602e-6
MA0003.10.621
MA0004.10.86
MA0006.10.114
MA0007.10.641
MA0009.10.141
MA0014.10.507
MA0017.10.898
MA0018.22.42761e-9
MA0019.10.476
MA0024.10.492
MA0025.10.0928
MA0027.10.709
MA0028.16.3011e-6
MA0029.10.398
MA0030.13.2401e-4
MA0031.11.50525e-5
MA0035.20.126
MA0038.10.161
MA0039.20.815
MA0040.10.679
MA0041.10.88
MA0042.10.396
MA0043.10.00128
MA0046.10.27
MA0047.20.0162
MA0048.10.871
MA0050.12.39333e-8
MA0051.11.55356e-4
MA0052.10.00705
MA0055.10.775
MA0057.10.508
MA0058.10.658
MA0059.10.656
MA0060.10.502
MA0061.14.8412e-4
MA0062.27.58052e-21
MA0065.20.344
MA0066.10.334
MA0067.10.00705
MA0068.10.824
MA0069.10.99
MA0070.10.924
MA0071.10.922
MA0072.10.0548
MA0073.10.825
MA0074.10.472
MA0076.11.73226e-8
MA0077.10.0295
MA0078.10.674
MA0079.20.651
MA0080.29.00694e-12
MA0081.10.00693
MA0083.10.186
MA0084.10.502
MA0087.10.72
MA0088.10.383
MA0090.12.3983e-4
MA0091.10.348
MA0092.10.928
MA0093.10.908
MA0099.20.0633
MA0100.10.429
MA0101.10.0746
MA0102.20.986
MA0103.10.448
MA0104.20.116
MA0105.15.34104e-6
MA0106.10.104
MA0107.10.135
MA0108.27.05642e-5
MA0111.10.532
MA0112.20.906
MA0113.10.802
MA0114.10.975
MA0115.10.458
MA0116.10.00214
MA0117.10.0322
MA0119.10.297
MA0122.10.406
MA0124.10.355
MA0125.10.231
MA0131.10.0913
MA0135.10.277
MA0136.12.21808e-24
MA0137.20.672
MA0138.20.179
MA0139.10.038
MA0140.10.0816
MA0141.10.308
MA0142.10.35
MA0143.10.297
MA0144.10.903
MA0145.10.0604
MA0146.10.772
MA0147.10.141
MA0148.10.0891
MA0149.10.283
MA0150.10.748
MA0152.10.0186
MA0153.10.346
MA0154.10.204
MA0155.10.262
MA0156.12.91752e-22
MA0157.13.68816e-4
MA0159.10.541
MA0160.10.873
MA0162.10.449
MA0163.14.26893e-5
MA0164.10.617
MA0258.10.889
MA0259.10.221



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: CNhs13237

Novel motifP-value
10.553
100.0187
1000.9
1010.344
1020.988
1030.535
1040.63
1050.241
1060.505
1070.0101
1080.516
1090.157
110.292
1100.922
1110.937
1120.882
1130.28
1140.637
1150.234
1160.131
1170.00243
1180.396
1190.378
120.6
1201
1210.962
1220.774
1230.0566
1240.633
1250.669
1260.408
1270.945
1280.662
1290.902
130.545
1300.37
1310.765
1320.274
1330.655
1340.91
1350.995
1360.856
1370.0186
1380.459
1390.0549
140.61
1400.196
1410.853
1420.622
1430.00161
1440.944
1450.968
1460.462
1470.0151
1480.255
1490.528
150.175
1500.727
1510.674
1520.511
1530.877
1540.459
1550.0403
1560.321
1570.332
1580.0163
1590.303
160.533
1600.185
1610.913
1620.0438
1630.388
1640.143
1650.517
1660.501
1670.287
1680.531
1690.22
170.728
180.863
190.0447
20.425
200.332
210.826
220.402
230.529
240.783
250.0806
260.687
270.627
280.453
290.027
30.303
300.128
310.714
320.033
330.16
340.376
350.235
360.0301
370.193
380.728
390.258
40.706
400.638
410.0926
420.183
430.556
440.771
450.24
460.63
470.305
480.534
490.231
50.343
500.492
510.87
520.399
530.613
540.995
550.725
560.922
570.964
580.151
590.562
60.761
600.551
610.0765
620.182
630.823
640.715
650.701
660.781
670.526
680.823
690.697
70.346
700.0975
710.0904
720.133
730.567
740.682
750.0198
760.156
770.0169
780.823
790.793
80.589
800.0021
810.56
820.313
830.457
840.651
850.699
860.0998
870.866
880.837
890.0542
90.924
900.142
910.844
920.857
930.516
940.19
950.00552
960.35
970.424
980.233
991.44131e-5



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: CNhs13237


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)
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)
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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