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FF:11792-124C1: 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- memory 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 number13
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-Basophils0.0887
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.139
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-lymphoma0.421
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-Whole0.127
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: CNhs13215

Jaspar motifP-value
MA0002.21.76451e-8
MA0003.10.85
MA0004.10.805
MA0006.10.534
MA0007.10.576
MA0009.10.249
MA0014.10.783
MA0017.10.0929
MA0018.20.885
MA0019.10.512
MA0024.10.0307
MA0025.10.0802
MA0027.10.602
MA0028.11.6218e-5
MA0029.10.495
MA0030.10.385
MA0031.10.48
MA0035.20.0416
MA0038.10.157
MA0039.20.772
MA0040.10.207
MA0041.10.317
MA0042.10.697
MA0043.10.0482
MA0046.10.0991
MA0047.20.411
MA0048.10.786
MA0050.16.159e-7
MA0051.10.0095
MA0052.10.00323
MA0055.10.918
MA0057.10.994
MA0058.10.937
MA0059.10.381
MA0060.10.415
MA0061.10.0923
MA0062.21.10158e-15
MA0065.20.029
MA0066.10.271
MA0067.10.976
MA0068.10.124
MA0069.10.807
MA0070.10.582
MA0071.10.427
MA0072.10.707
MA0073.10.786
MA0074.10.522
MA0076.12.67799e-8
MA0077.10.0421
MA0078.10.903
MA0079.20.494
MA0080.21.08937e-12
MA0081.10.0239
MA0083.10.0438
MA0084.10.894
MA0087.10.448
MA0088.10.0316
MA0090.11.98398e-4
MA0091.10.824
MA0092.10.492
MA0093.10.779
MA0099.23.97943e-4
MA0100.10.216
MA0101.10.709
MA0102.20.322
MA0103.10.0643
MA0104.20.179
MA0105.13.65937e-5
MA0106.10.808
MA0107.10.253
MA0108.23.46494e-14
MA0111.10.055
MA0112.20.169
MA0113.10.915
MA0114.10.154
MA0115.10.389
MA0116.11.87927e-5
MA0117.10.781
MA0119.10.489
MA0122.10.817
MA0124.10.828
MA0125.10.723
MA0131.10.259
MA0135.10.0888
MA0136.14.09859e-24
MA0137.20.218
MA0138.20.178
MA0139.10.00516
MA0140.10.0538
MA0141.10.464
MA0142.10.455
MA0143.10.0998
MA0144.10.24
MA0145.10.796
MA0146.10.163
MA0147.10.152
MA0148.10.989
MA0149.10.0749
MA0150.10.305
MA0152.10.0278
MA0153.10.105
MA0154.10.0165
MA0155.10.717
MA0156.12.32561e-22
MA0157.10.138
MA0159.10.222
MA0160.10.364
MA0162.10.665
MA0163.15.84504e-12
MA0164.10.685
MA0258.10.0763
MA0259.10.387



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: CNhs13215

Novel motifP-value
10.113
100.0103
1000.767
1010.0955
1020.522
1030.16
1040.679
1050.154
1060.596
1070.478
1080.675
1090.0406
110.0402
1100.411
1110.384
1120.122
1130.474
1140.238
1150.116
1160.582
1170.0064
1180.4
1190.539
120.509
1200.482
1210.634
1220.326
1234.42326e-4
1240.0599
1250.978
1260.434
1270.377
1280.663
1290.161
130.415
1300.889
1310.803
1320.959
1330.247
1340.702
1350.748
1360.657
1370.0709
1380.289
1390.268
140.396
1400.0213
1410.655
1420.952
1430.00139
1440.479
1450.248
1460.442
1470.0258
1480.0669
1490.807
150.0998
1500.463
1510.6
1520.329
1530.982
1540.724
1550.0143
1560.585
1570.0644
1580.289
1590.383
160.623
1600.559
1610.175
1620.166
1630.448
1640.118
1650.183
1660.797
1670.269
1680.2
1690.348
170.872
180.611
190.609
20.909
200.758
210.312
220.989
230.54
240.586
250.0645
260.123
270.155
280.56
290.0176
30.0464
300.198
310.932
320.307
330.528
340.958
350.185
360.0248
370.229
380.666
390.318
40.609
400.348
410.485
420.0647
430.444
440.268
450.499
460.0895
470.0115
480.0349
490.161
50.565
500.786
510.609
520.298
530.216
540.806
550.552
560.465
570.206
580.111
590.31
60.673
600.514
610.0812
620.0481
630.514
640.128
650.916
660.819
670.924
680.688
690.864
70.243
700.0586
710.0351
720.0561
730.552
740.379
750.0162
760.434
770.754
780.0296
790.239
80.431
800.0948
810.42
820.139
830.614
840.196
850.705
860.168
870.362
880.749
890.682
90.761
900.0166
910.636
920.395
930.205
940.107
950.0103
960.0541
970.311
980.303
990.247



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: CNhs13215


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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