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FF:11780-124A7: 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+ naive regulatory T cells, 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 number1
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-Basophils0.661
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.117
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: CNhs13238

Jaspar motifP-value
MA0002.27.24755e-4
MA0003.10.437
MA0004.10.701
MA0006.10.0399
MA0007.10.962
MA0009.10.192
MA0014.10.384
MA0017.10.907
MA0018.22.27826e-10
MA0019.10.403
MA0024.10.941
MA0025.10.0674
MA0027.10.431
MA0028.16.29309e-8
MA0029.10.761
MA0030.10.00164
MA0031.12.57282e-5
MA0035.20.136
MA0038.10.246
MA0039.20.491
MA0040.10.853
MA0041.10.603
MA0042.10.666
MA0043.12.61068e-4
MA0046.10.667
MA0047.20.0671
MA0048.10.708
MA0050.11.61226e-4
MA0051.10.02
MA0052.10.0256
MA0055.10.441
MA0057.10.437
MA0058.10.604
MA0059.10.705
MA0060.10.818
MA0061.10.079
MA0062.29.54976e-23
MA0065.20.625
MA0066.10.738
MA0067.10.00542
MA0068.10.971
MA0069.10.772
MA0070.10.937
MA0071.10.876
MA0072.10.214
MA0073.10.937
MA0074.10.132
MA0076.12.51449e-10
MA0077.10.0359
MA0078.10.678
MA0079.20.672
MA0080.23.06307e-10
MA0081.10.00934
MA0083.10.0384
MA0084.10.271
MA0087.10.764
MA0088.10.331
MA0090.12.35643e-4
MA0091.10.254
MA0092.10.599
MA0093.10.757
MA0099.28.4987e-5
MA0100.10.459
MA0101.10.895
MA0102.20.59
MA0103.10.279
MA0104.20.0698
MA0105.10.00402
MA0106.10.0828
MA0107.10.937
MA0108.26.36676e-6
MA0111.10.454
MA0112.20.645
MA0113.10.779
MA0114.10.736
MA0115.10.688
MA0116.10.0142
MA0117.10.0351
MA0119.10.0918
MA0122.10.53
MA0124.10.329
MA0125.10.274
MA0131.10.0283
MA0135.10.369
MA0136.13.30483e-24
MA0137.20.692
MA0138.20.188
MA0139.10.0892
MA0140.10.223
MA0141.10.273
MA0142.10.102
MA0143.10.204
MA0144.10.707
MA0145.10.0247
MA0146.10.7
MA0147.10.0774
MA0148.10.279
MA0149.10.285
MA0150.10.283
MA0152.10.00359
MA0153.10.465
MA0154.10.698
MA0155.10.141
MA0156.18.32959e-20
MA0157.16.31214e-5
MA0159.10.643
MA0160.10.821
MA0162.10.165
MA0163.15.41096e-4
MA0164.10.839
MA0258.10.726
MA0259.10.0886



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: CNhs13238

Novel motifP-value
10.699
100.0238
1000.615
1010.488
1020.654
1030.873
1040.866
1050.371
1060.705
1071.49079e-4
1080.391
1090.278
110.511
1100.853
1110.873
1120.974
1130.694
1140.997
1150.359
1160.0613
1170.00361
1180.352
1190.0766
120.826
1200.954
1210.805
1220.567
1230.0281
1240.71
1250.224
1260.914
1270.982
1280.0988
1290.886
130.543
1300.543
1310.256
1320.296
1330.965
1340.843
1350.912
1360.755
1370.0492
1380.445
1390.198
140.764
1400.27
1410.642
1420.54
1430.0101
1440.813
1450.308
1460.792
1470.0197
1480.659
1490.41
150.401
1500.861
1510.902
1520.241
1530.871
1540.553
1550.0107
1560.911
1570.54
1580.00486
1590.589
160.373
1600.13
1610.788
1620.00676
1630.666
1640.111
1650.874
1660.214
1670.0838
1680.88
1690.0921
170.519
180.686
190.0429
20.226
200.296
210.841
220.374
230.27
240.646
250.101
260.961
270.806
280.581
290.0323
30.462
300.156
310.616
320.0273
330.126
340.339
350.475
360.0354
370.572
380.767
390.178
40.775
400.814
410.0803
420.253
430.733
440.977
450.188
460.84
470.36
480.682
490.322
50.666
500.513
510.969
520.273
530.678
540.834
550.829
560.747
570.756
580.18
590.518
60.692
600.9
610.0885
620.287
630.765
640.695
650.629
660.927
670.841
680.483
690.956
70.466
700.271
710.209
720.12
730.915
740.69
750.00675
760.0498
770.00563
780.358
790.345
80.346
800.0205
810.674
820.432
830.99
840.613
850.226
860.2
870.826
880.996
890.0403
90.909
900.188
910.962
920.666
930.849
940.312
950.0101
960.638
970.301
980.377
996.80335e-6



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: CNhs13238


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)
0000813 (memory T cell)
0000815 (regulatory T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor 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)
0002678 (memory 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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