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FF:11908-125F9: 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 17:36, 29 March 2012


Name:CD4+CD25+CD45RA- memory regulatory T cells, donor3
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 number37-38
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-Basophils1.053
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.135
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
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: CNhs13538

Jaspar motifP-value
MA0002.22.51936e-6
MA0003.10.741
MA0004.10.867
MA0006.10.229
MA0007.10.814
MA0009.10.0557
MA0014.10.971
MA0017.10.282
MA0018.27.00442e-5
MA0019.10.798
MA0024.10.653
MA0025.10.549
MA0027.10.77
MA0028.12.95516e-4
MA0029.10.155
MA0030.10.0448
MA0031.10.00341
MA0035.20.152
MA0038.10.0654
MA0039.20.738
MA0040.10.64
MA0041.10.46
MA0042.10.632
MA0043.10.125
MA0046.10.186
MA0047.20.0988
MA0048.10.54
MA0050.16.58335e-9
MA0051.10.00129
MA0052.10.00363
MA0055.10.626
MA0057.10.571
MA0058.10.731
MA0059.10.533
MA0060.10.0549
MA0061.10.01
MA0062.22.44978e-14
MA0065.20.153
MA0066.10.143
MA0067.10.03
MA0068.10.114
MA0069.10.89
MA0070.10.58
MA0071.10.981
MA0072.10.175
MA0073.10.943
MA0074.10.377
MA0076.12.78137e-6
MA0077.10.0167
MA0078.10.625
MA0079.20.276
MA0080.24.10713e-11
MA0081.10.0327
MA0083.10.045
MA0084.10.41
MA0087.10.537
MA0088.10.387
MA0090.11.09531e-4
MA0091.10.654
MA0092.10.944
MA0093.10.949
MA0099.20.0099
MA0100.10.472
MA0101.10.776
MA0102.20.684
MA0103.10.147
MA0104.20.212
MA0105.12.72254e-6
MA0106.10.367
MA0107.10.935
MA0108.22.05801e-10
MA0111.10.0937
MA0112.20.272
MA0113.10.626
MA0114.10.453
MA0115.10.576
MA0116.14.75632e-5
MA0117.10.153
MA0119.10.969
MA0122.10.631
MA0124.10.364
MA0125.10.282
MA0131.10.241
MA0135.10.272
MA0136.18.58148e-22
MA0137.20.859
MA0138.20.334
MA0139.10.0275
MA0140.10.0833
MA0141.10.531
MA0142.10.389
MA0143.10.506
MA0144.10.885
MA0145.10.511
MA0146.10.66
MA0147.10.179
MA0148.10.417
MA0149.10.11
MA0150.10.862
MA0152.10.0144
MA0153.10.2
MA0154.10.035
MA0155.10.438
MA0156.19.58504e-17
MA0157.10.0022
MA0159.10.217
MA0160.10.982
MA0162.10.789
MA0163.11.45754e-7
MA0164.10.628
MA0258.10.284
MA0259.10.302



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: CNhs13538

Novel motifP-value
10.194
100.00718
1000.766
1010.0728
1020.889
1030.297
1040.889
1050.432
1060.551
1070.03
1080.733
1090.192
110.154
1100.694
1110.318
1120.462
1130.232
1140.265
1150.372
1160.55
1170.00418
1180.338
1190.916
120.799
1200.996
1210.638
1220.63
1230.00101
1240.321
1250.94
1260.434
1270.742
1280.851
1290.985
130.549
1300.307
1310.786
1320.329
1330.696
1340.733
1350.641
1360.896
1370.0624
1380.159
1390.047
140.371
1400.104
1410.354
1420.503
1430.0061
1440.982
1450.511
1460.652
1470.053
1480.0568
1490.594
150.0983
1500.797
1510.569
1520.255
1530.653
1540.561
1550.017
1560.524
1570.311
1580.00765
1590.934
160.946
1600.625
1610.71
1620.0532
1630.74
1640.0735
1650.247
1660.445
1670.175
1680.718
1690.998
170.931
180.605
190.339
20.64
200.659
210.729
220.639
230.736
240.727
250.0531
260.271
270.416
280.478
290.0123
30.118
300.157
310.883
320.225
330.229
340.437
350.136
360.0256
370.204
380.987
390.352
40.801
400.566
410.137
420.0974
430.365
440.53
450.391
460.209
470.101
480.242
490.0828
50.333
500.441
510.64
520.363
530.452
540.872
550.627
560.837
570.59
580.0791
590.86
60.987
600.434
610.118
620.057
630.86
640.416
650.925
660.835
670.951
680.992
690.896
70.221
700.038
710.0302
720.0642
730.866
740.384
750.0243
760.159
770.102
780.272
790.829
80.967
800.029
810.282
820.0886
830.771
840.696
850.773
860.108
870.519
880.775
890.197
90.957
900.00969
910.489
920.31
930.561
940.118
950.132
960.122
970.338
980.0972
993.32198e-4



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: CNhs13538


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)
0000792 (CD4-positive, CD25-positive, alpha-beta regulatory T cell)
0000815 (regulatory T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor 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)
0002677 (naive regulatory T cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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