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FF:11782-124A9: 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 17:29, 29 March 2012


Name:CD4+CD25+CD45RA- memory 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 number2
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-Basophils1.086
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.116
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-lymphoma-0.177
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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-Whole0.112
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: CNhs13195

Jaspar motifP-value
MA0002.21.11912e-5
MA0003.10.729
MA0004.10.871
MA0006.10.205
MA0007.10.958
MA0009.10.0913
MA0014.10.863
MA0017.10.734
MA0018.21.12636e-7
MA0019.10.936
MA0024.10.558
MA0025.10.465
MA0027.10.751
MA0028.12.2847e-4
MA0029.10.158
MA0030.10.0551
MA0031.10.00221
MA0035.20.101
MA0038.10.103
MA0039.20.998
MA0040.10.84
MA0041.10.291
MA0042.10.878
MA0043.10.0249
MA0046.10.214
MA0047.20.217
MA0048.10.859
MA0050.11.13924e-6
MA0051.10.0186
MA0052.10.00169
MA0055.10.931
MA0057.10.58
MA0058.10.783
MA0059.10.672
MA0060.10.225
MA0061.10.0114
MA0062.29.03569e-14
MA0065.20.203
MA0066.10.191
MA0067.10.01
MA0068.10.864
MA0069.10.66
MA0070.10.468
MA0071.10.683
MA0072.10.122
MA0073.10.94
MA0074.10.32
MA0076.16.12756e-6
MA0077.10.0404
MA0078.10.673
MA0079.20.255
MA0080.26.021e-11
MA0081.10.0228
MA0083.10.095
MA0084.10.34
MA0087.10.533
MA0088.10.395
MA0090.19.94479e-5
MA0091.10.684
MA0092.10.979
MA0093.10.985
MA0099.20.0058
MA0100.10.716
MA0101.10.735
MA0102.20.456
MA0103.10.177
MA0104.20.203
MA0105.12.33971e-6
MA0106.10.157
MA0107.10.939
MA0108.29.26537e-8
MA0111.10.186
MA0112.20.359
MA0113.10.663
MA0114.10.793
MA0115.10.559
MA0116.12.03247e-4
MA0117.10.0859
MA0119.10.699
MA0122.10.645
MA0124.10.284
MA0125.10.16
MA0131.10.106
MA0135.10.257
MA0136.14.47701e-23
MA0137.20.751
MA0138.20.274
MA0139.10.0554
MA0140.10.106
MA0141.10.678
MA0142.10.204
MA0143.10.26
MA0144.10.805
MA0145.10.233
MA0146.10.655
MA0147.10.175
MA0148.10.449
MA0149.10.0704
MA0150.10.768
MA0152.10.00803
MA0153.10.123
MA0154.10.0651
MA0155.10.359
MA0156.12.4451e-16
MA0157.19.66724e-4
MA0159.10.292
MA0160.10.795
MA0162.10.943
MA0163.11.33366e-7
MA0164.10.496
MA0258.10.367
MA0259.10.259



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: CNhs13195

Novel motifP-value
10.305
100.00816
1000.502
1010.215
1020.732
1030.689
1040.924
1050.252
1060.38
1070.0201
1080.923
1090.114
110.174
1100.811
1110.531
1120.598
1130.345
1140.288
1150.39
1160.402
1170.00386
1180.315
1190.853
120.754
1200.922
1210.655
1220.57
1232.3267e-4
1240.319
1250.676
1260.527
1270.821
1280.966
1290.909
130.367
1300.23
1310.973
1320.287
1330.984
1340.925
1350.981
1360.884
1370.0498
1380.33
1390.0833
140.503
1400.0501
1410.504
1420.236
1430.00179
1440.995
1450.683
1460.8
1470.0412
1480.0971
1490.558
150.11
1500.753
1510.528
1520.543
1530.631
1540.464
1550.0175
1560.552
1570.181
1580.0275
1590.242
160.723
1600.523
1610.805
1620.0688
1630.553
1640.0462
1650.573
1660.355
1670.101
1680.914
1690.751
170.893
180.846
190.231
20.465
200.372
210.676
220.536
230.605
240.674
250.0775
260.299
270.649
280.578
290.00613
30.177
300.0906
310.869
320.146
330.168
340.344
350.217
360.0212
370.171
380.97
390.329
40.843
400.425
410.148
420.115
430.378
440.719
450.283
460.312
470.133
480.26
490.123
50.386
500.415
510.724
520.474
530.469
540.931
550.936
560.911
570.481
580.104
590.894
60.993
600.441
610.122
620.122
630.895
640.442
650.885
660.702
670.997
680.888
690.862
70.293
700.0598
710.0272
720.0522
730.48
740.891
750.0144
760.0912
770.0426
780.12
790.576
80.866
800.0579
810.342
820.0892
830.826
840.383
850.986
860.154
870.876
880.918
890.121
90.815
900.0163
910.633
920.365
930.995
940.176
950.0296
960.277
970.306
980.11
992.53403e-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: CNhs13195


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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