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Revision as of 20:46, 15 May 2017

Name:CD4+CD25-CD45RA+ naive conventional T cells, donor1
Species:Human (Homo sapiens)
Library ID:CNhs13223
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7
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 number3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004701
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13223 CAGE DRX008190 DRR009062
Accession ID Hg19

Library idBAMCTSS
CNhs13223 DRZ000487 DRZ001872
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
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C81-trachea-salivary-throat-aorta-eye-submaxillary-parotid0
C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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-Whole0.0601
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



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: CNhs13223

Jaspar motifP-value
MA0002.26.77667e-4
MA0003.10.39
MA0004.10.922
MA0006.10.0583
MA0007.10.888
MA0009.10.279
MA0014.10.598
MA0017.10.615
MA0018.26.48717e-8
MA0019.10.931
MA0024.10.592
MA0025.10.349
MA0027.10.744
MA0028.19.56932e-5
MA0029.10.328
MA0030.10.0237
MA0031.11.1291e-4
MA0035.20.329
MA0038.10.107
MA0039.20.915
MA0040.10.675
MA0041.10.311
MA0042.10.94
MA0043.10.018
MA0046.10.179
MA0047.20.182
MA0048.10.769
MA0050.11.82027e-4
MA0051.10.0175
MA0052.10.00643
MA0055.10.98
MA0057.10.489
MA0058.10.967
MA0059.10.807
MA0060.10.355
MA0061.10.292
MA0062.24.09262e-16
MA0065.20.525
MA0066.10.833
MA0067.10.0334
MA0068.10.378
MA0069.10.97
MA0070.10.687
MA0071.10.596
MA0072.10.612
MA0073.10.976
MA0074.10.447
MA0076.16.69874e-7
MA0077.10.0279
MA0078.10.75
MA0079.20.566
MA0080.21.07167e-10
MA0081.10.0168
MA0083.10.0109
MA0084.10.333
MA0087.10.574
MA0088.10.273
MA0090.15.06345e-4
MA0091.10.539
MA0092.10.759
MA0093.10.943
MA0099.21.98773e-9
MA0100.10.567
MA0101.10.402
MA0102.20.596
MA0103.10.234
MA0104.20.0696
MA0105.10.00649
MA0106.10.0736
MA0107.10.27
MA0108.21.32703e-9
MA0111.10.217
MA0112.20.61
MA0113.10.568
MA0114.10.781
MA0115.10.593
MA0116.10.00621
MA0117.10.0958
MA0119.10.553
MA0122.10.666
MA0124.10.559
MA0125.10.0956
MA0131.10.0642
MA0135.10.075
MA0136.14.15826e-22
MA0137.20.515
MA0138.20.33
MA0139.10.103
MA0140.10.372
MA0141.10.184
MA0142.10.0597
MA0143.10.0939
MA0144.10.469
MA0145.10.0315
MA0146.10.779
MA0147.10.0893
MA0148.10.31
MA0149.10.248
MA0150.10.0527
MA0152.17.37445e-4
MA0153.10.229
MA0154.10.487
MA0155.10.281
MA0156.11.06941e-18
MA0157.11.03947e-4
MA0159.10.837
MA0160.10.434
MA0162.10.21
MA0163.12.05226e-5
MA0164.10.891
MA0258.10.964
MA0259.10.0969



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: CNhs13223

Novel motifP-value
10.542
100.0201
1000.587
1010.23
1020.795
1030.877
1040.924
1050.536
1060.787
1076.93466e-4
1080.557
1090.348
110.372
1100.926
1110.616
1120.859
1130.431
1140.641
1150.23
1160.201
1170.00193
1180.33
1190.115
120.767
1200.709
1210.847
1220.764
1235.31024e-4
1240.596
1250.564
1260.893
1270.989
1280.376
1290.737
130.724
1300.343
1310.312
1320.572
1330.821
1340.596
1350.768
1360.705
1370.0295
1380.348
1390.0912
140.699
1400.266
1410.478
1420.356
1430.00882
1440.838
1450.629
1460.911
1470.0128
1480.406
1490.298
150.318
1500.883
1510.515
1520.169
1530.756
1540.308
1550.0216
1560.976
1570.475
1580.00367
1590.891
160.456
1600.334
1610.93
1620.0961
1630.351
1640.11
1650.575
1660.431
1670.0944
1680.93
1690.134
170.459
180.636
190.0558
20.284
200.364
210.523
220.301
230.304
240.656
250.112
260.938
270.638
280.651
290.0364
30.255
300.0925
310.602
320.0189
330.219
340.275
350.132
360.0326
370.4
380.77
390.134
40.583
400.942
410.23
420.166
430.663
440.936
450.213
460.587
470.242
480.469
490.142
50.591
500.443
510.96
520.236
530.567
540.841
550.808
560.968
570.844
580.19
590.409
60.781
600.982
610.097
620.209
630.894
640.586
650.63
660.695
670.715
680.752
690.846
70.532
700.124
710.151
720.161
730.778
740.72
750.00825
760.12
770.0096
780.643
790.756
80.635
800.0324
810.395
820.256
830.593
840.619
850.318
860.292
870.421
880.972
890.0582
90.753
900.0332
910.574
920.92
930.899
940.379
950.205
960.371
970.346
980.287
991.40109e-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: CNhs13223


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)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)

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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