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FF:11791-124B9: 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 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 number11
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-Basophils0.111
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.137
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-lymphoma0.325
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13202

Jaspar motifP-value
MA0002.22.13302e-9
MA0003.10.705
MA0004.10.822
MA0006.10.445
MA0007.10.678
MA0009.10.283
MA0014.10.939
MA0017.10.0534
MA0018.20.341
MA0019.10.729
MA0024.10.253
MA0025.10.192
MA0027.10.663
MA0028.13.63396e-4
MA0029.10.375
MA0030.10.593
MA0031.10.296
MA0035.20.044
MA0038.10.15
MA0039.20.54
MA0040.10.155
MA0041.10.135
MA0042.10.487
MA0043.10.0218
MA0046.10.194
MA0047.20.373
MA0048.10.706
MA0050.11.90419e-6
MA0051.10.0131
MA0052.10.0032
MA0055.10.936
MA0057.10.842
MA0058.10.935
MA0059.10.367
MA0060.10.847
MA0061.10.0141
MA0062.23.05954e-12
MA0065.20.0209
MA0066.10.116
MA0067.10.767
MA0068.10.11
MA0069.10.511
MA0070.10.647
MA0071.10.444
MA0072.10.839
MA0073.10.797
MA0074.10.726
MA0076.16.13786e-6
MA0077.10.0636
MA0078.10.578
MA0079.20.34
MA0080.21.04803e-13
MA0081.10.0235
MA0083.10.00923
MA0084.10.805
MA0087.10.236
MA0088.10.0457
MA0090.17.31704e-4
MA0091.10.649
MA0092.10.576
MA0093.10.767
MA0099.21.41911e-4
MA0100.10.135
MA0101.10.773
MA0102.20.367
MA0103.10.0666
MA0104.20.185
MA0105.11.61814e-6
MA0106.10.979
MA0107.10.953
MA0108.27.41042e-15
MA0111.10.088
MA0112.20.0383
MA0113.10.833
MA0114.10.159
MA0115.10.447
MA0116.11.73536e-5
MA0117.10.835
MA0119.10.722
MA0122.10.9
MA0124.10.63
MA0125.10.363
MA0131.10.462
MA0135.10.0966
MA0136.11.08459e-24
MA0137.20.193
MA0138.20.635
MA0139.10.0184
MA0140.10.0702
MA0141.10.597
MA0142.10.461
MA0143.10.204
MA0144.10.291
MA0145.10.748
MA0146.10.302
MA0147.10.151
MA0148.10.847
MA0149.10.0909
MA0150.10.122
MA0152.10.0154
MA0153.10.552
MA0154.10.00541
MA0155.10.793
MA0156.13.14632e-21
MA0157.10.066
MA0159.10.209
MA0160.10.305
MA0162.10.725
MA0163.11.27238e-14
MA0164.10.794
MA0258.10.0207
MA0259.10.444



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: CNhs13202

Novel motifP-value
10.117
100.0102
1000.838
1010.141
1020.64
1030.131
1040.582
1050.114
1060.382
1070.552
1080.674
1090.0662
110.0401
1100.348
1110.259
1120.163
1130.532
1140.165
1150.0757
1160.982
1170.0112
1180.472
1190.494
120.648
1200.511
1210.859
1220.366
1230.00547
1240.0771
1250.886
1260.47
1270.344
1280.538
1290.115
130.458
1300.951
1310.517
1320.743
1330.244
1340.594
1350.613
1360.772
1370.0878
1380.201
1390.279
140.59
1400.0309
1410.547
1420.683
1438.27297e-4
1440.622
1450.222
1460.383
1470.091
1480.0356
1490.96
150.108
1500.646
1510.512
1520.319
1530.788
1540.778
1550.0196
1560.565
1570.196
1580.0732
1590.73
160.545
1600.249
1610.145
1620.126
1630.907
1640.147
1650.13
1660.659
1670.138
1680.223
1690.368
170.79
180.569
190.767
20.791
200.963
210.271
220.877
230.732
240.712
250.0673
260.149
270.0832
280.577
290.0178
30.0343
300.299
310.897
320.552
330.334
340.903
350.104
360.0174
370.212
380.597
390.274
40.607
400.32
410.402
420.0618
430.314
440.311
450.66
460.0483
470.0106
480.056
490.118
50.417
500.866
510.479
520.397
530.29
540.699
550.537
560.408
570.264
580.0827
590.264
60.795
600.38
610.14
620.0263
630.512
640.112
650.733
660.943
670.743
680.75
690.815
70.161
700.0559
710.0198
720.0963
730.69
740.689
750.0156
760.543
770.648
780.026
790.239
80.383
800.0261
810.436
820.0597
830.505
840.278
850.829
860.267
870.897
880.898
890.73
90.68
900.0148
910.398
920.289
930.267
940.0538
950.0621
960.0771
970.341
980.316
990.27



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: CNhs13202


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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