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FF:11913-125G5: 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+ naive conventional 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 number53-54
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-Basophils0.0661
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0235
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-lymphoma0.322
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: CNhs13813

Jaspar motifP-value
MA0002.21.91686e-5
MA0003.10.79
MA0004.10.742
MA0006.10.515
MA0007.10.951
MA0009.10.488
MA0014.10.896
MA0017.10.29
MA0018.20.445
MA0019.10.0568
MA0024.10.0591
MA0025.10.0779
MA0027.10.408
MA0028.16.95e-4
MA0029.10.415
MA0030.10.126
MA0031.10.965
MA0035.20.315
MA0038.10.0712
MA0039.20.489
MA0040.10.177
MA0041.10.204
MA0042.10.41
MA0043.10.0423
MA0046.10.0366
MA0047.20.825
MA0048.10.608
MA0050.16.58875e-7
MA0051.10.0137
MA0052.10.0109
MA0055.10.626
MA0057.10.78
MA0058.10.842
MA0059.10.48
MA0060.10.722
MA0061.10.0911
MA0062.21.4193e-9
MA0065.20.0697
MA0066.10.379
MA0067.10.879
MA0068.10.618
MA0069.10.893
MA0070.10.582
MA0071.10.558
MA0072.10.865
MA0073.10.845
MA0074.10.738
MA0076.11.19712e-4
MA0077.10.0652
MA0078.10.933
MA0079.20.291
MA0080.28.23117e-9
MA0081.10.0874
MA0083.10.0545
MA0084.10.877
MA0087.10.385
MA0088.10.0508
MA0090.10.00169
MA0091.10.928
MA0092.10.838
MA0093.10.665
MA0099.27.40104e-6
MA0100.10.708
MA0101.10.617
MA0102.20.173
MA0103.10.0713
MA0104.20.276
MA0105.12.20974e-5
MA0106.10.941
MA0107.10.278
MA0108.23.27146e-10
MA0111.10.054
MA0112.20.12
MA0113.10.956
MA0114.10.25
MA0115.10.536
MA0116.13.39379e-5
MA0117.10.993
MA0119.10.853
MA0122.10.825
MA0124.10.428
MA0125.10.399
MA0131.10.201
MA0135.10.0208
MA0136.12.27431e-14
MA0137.20.696
MA0138.20.294
MA0139.10.0281
MA0140.10.577
MA0141.10.564
MA0142.10.276
MA0143.10.112
MA0144.10.965
MA0145.10.512
MA0146.10.104
MA0147.10.23
MA0148.10.58
MA0149.10.0443
MA0150.10.164
MA0152.10.0462
MA0153.10.0946
MA0154.10.0362
MA0155.10.551
MA0156.11.48867e-10
MA0157.10.563
MA0159.10.462
MA0160.10.67
MA0162.10.873
MA0163.13.19359e-12
MA0164.10.985
MA0258.10.0195
MA0259.10.497



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: CNhs13813

Novel motifP-value
10.0707
100.00359
1000.423
1010.0518
1020.571
1030.775
1040.741
1050.409
1060.299
1070.725
1080.886
1090.12
110.0323
1100.336
1110.222
1120.274
1130.29
1140.413
1150.155
1160.342
1170.0031
1180.41
1190.277
120.721
1200.749
1210.781
1220.863
1232.38734e-7
1240.156
1250.834
1260.793
1270.719
1280.525
1290.381
130.328
1300.569
1310.634
1320.48
1330.459
1340.51
1350.639
1360.827
1370.355
1380.192
1390.267
140.473
1400.046
1410.472
1420.62
1430.0133
1440.362
1450.106
1460.831
1470.187
1480.059
1490.884
150.233
1500.487
1510.582
1520.175
1530.991
1540.389
1550.0646
1560.746
1570.299
1580.187
1590.957
160.651
1600.3
1610.0627
1620.503
1630.241
1640.0988
1650.622
1660.913
1670.134
1680.734
1690.251
170.796
180.995
190.794
20.922
200.556
210.143
220.8
230.755
240.939
250.185
260.0342
270.324
280.661
290.0288
30.0342
300.0806
310.96
320.537
330.648
340.98
350.22
360.0229
370.309
380.537
390.597
40.945
400.348
410.878
420.0891
430.331
440.322
450.375
460.0767
470.018
480.0446
490.0638
50.777
500.953
510.686
520.436
530.0916
540.755
550.648
560.375
570.108
580.15
590.542
60.433
600.506
610.181
620.0776
630.338
640.109
650.726
660.746
670.608
680.939
690.928
70.363
700.124
710.0344
720.216
730.688
740.596
750.00928
760.214
770.723
780.0285
790.668
80.328
800.546
810.391
820.109
830.409
840.0366
850.919
860.206
870.993
880.841
890.315
90.862
900.0526
910.377
920.406
930.487
940.146
950.0436
960.2
970.19
980.346
990.452



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: CNhs13813


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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