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FF:11796-124C5: 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, 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 number21
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-Basophils0.584
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.126
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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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: CNhs13235

Jaspar motifP-value
MA0002.22.78023e-4
MA0003.10.559
MA0004.10.53
MA0006.10.0515
MA0007.10.977
MA0009.10.287
MA0014.10.372
MA0017.10.583
MA0018.25.8688e-9
MA0019.10.68
MA0024.10.659
MA0025.10.203
MA0027.10.34
MA0028.16.4926e-7
MA0029.10.568
MA0030.10.00335
MA0031.12.13902e-5
MA0035.20.151
MA0038.10.31
MA0039.20.821
MA0040.10.996
MA0041.10.419
MA0042.10.878
MA0043.10.0042
MA0046.10.558
MA0047.20.0638
MA0048.10.824
MA0050.11.77361e-4
MA0051.10.0262
MA0052.10.028
MA0055.10.264
MA0057.10.544
MA0058.10.459
MA0059.10.412
MA0060.10.689
MA0061.10.0817
MA0062.23.30555e-19
MA0065.20.193
MA0066.10.417
MA0067.10.0187
MA0068.10.826
MA0069.10.802
MA0070.10.819
MA0071.10.864
MA0072.10.317
MA0073.10.977
MA0074.10.173
MA0076.13.15179e-10
MA0077.10.0122
MA0078.10.9
MA0079.20.372
MA0080.21.71574e-9
MA0081.10.00893
MA0083.10.0232
MA0084.10.227
MA0087.10.813
MA0088.10.239
MA0090.16.68858e-4
MA0091.10.55
MA0092.10.904
MA0093.10.6
MA0099.24.44753e-5
MA0100.10.575
MA0101.10.969
MA0102.20.404
MA0103.10.155
MA0104.20.0573
MA0105.10.00152
MA0106.10.228
MA0107.10.754
MA0108.21.47548e-6
MA0111.10.386
MA0112.20.799
MA0113.10.863
MA0114.10.658
MA0115.10.857
MA0116.10.00622
MA0117.10.0608
MA0119.10.423
MA0122.10.41
MA0124.10.465
MA0125.10.105
MA0131.10.0614
MA0135.10.219
MA0136.13.33608e-21
MA0137.20.684
MA0138.20.321
MA0139.10.0949
MA0140.10.172
MA0141.10.48
MA0142.10.138
MA0143.10.215
MA0144.10.69
MA0145.10.0549
MA0146.10.602
MA0147.10.0619
MA0148.10.196
MA0149.10.151
MA0150.10.311
MA0152.10.0179
MA0153.10.356
MA0154.10.378
MA0155.10.329
MA0156.18.1356e-19
MA0157.18.34363e-5
MA0159.10.44
MA0160.10.944
MA0162.10.432
MA0163.13.18303e-6
MA0164.10.639
MA0258.10.703
MA0259.10.0898



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: CNhs13235

Novel motifP-value
10.466
100.0143
1000.472
1010.226
1020.918
1030.624
1040.815
1050.289
1060.962
1070.00273
1080.503
1090.185
110.28
1100.802
1110.828
1120.952
1130.609
1140.595
1150.194
1160.159
1170.00229
1180.229
1190.303
120.726
1200.939
1210.862
1220.77
1230.00466
1240.593
1250.249
1260.758
1270.768
1280.291
1290.936
130.455
1300.524
1310.501
1320.367
1330.652
1340.652
1350.945
1360.919
1370.115
1380.482
1390.0596
140.67
1400.184
1410.623
1420.217
1430.0123
1440.807
1450.656
1460.589
1470.0184
1480.343
1490.406
150.223
1500.911
1510.657
1520.235
1530.68
1540.466
1550.0127
1560.895
1570.47
1580.00352
1590.463
160.512
1600.455
1610.99
1620.0374
1630.36
1640.121
1650.826
1660.245
1670.139
1680.754
1690.309
170.6
180.708
190.0923
20.351
200.221
210.699
220.451
230.385
240.573
250.0833
260.754
270.755
280.594
290.0199
30.273
300.127
310.631
320.0441
330.138
340.344
350.302
360.0187
370.306
380.934
390.261
40.964
400.47
410.107
420.184
430.513
440.983
450.209
460.628
470.225
480.451
490.195
50.483
500.537
510.957
520.256
530.544
540.932
550.767
560.914
570.75
580.113
590.668
60.929
600.76
610.0748
620.144
630.981
640.567
650.788
660.846
670.91
680.436
690.549
70.351
700.154
710.115
720.15
730.822
740.54
750.0065
760.0649
770.0223
780.301
790.475
80.485
800.0118
810.561
820.253
830.771
840.555
850.332
860.206
870.573
880.997
890.0734
90.979
900.151
910.856
920.967
930.74
940.269
950.00981
960.619
970.273
980.28
991.07317e-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: CNhs13235


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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