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|library_id=CNhs10853
|library_id=CNhs10853
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|library_id_phase_based=2:CNhs10853
|name="CD4+ T Cells, donor1"
|name=CD4+ T Cells, donor1
|namespace=FANTOM5
|namespace=FANTOM5
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|part_of=
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|profile_hcage="CNhs10853,LSID702,release008,COMPLETED"
|profile_hcage=CNhs10853,LSID702,release008,COMPLETED
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Line 72: Line 72:
|sample_cell_line=
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_lot=N/A
|sample_cell_type="t cell, CD4+"
|sample_cell_type=t cell, CD4+
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=3HBiomedical
|sample_company=3HBiomedical

Revision as of 18:37, 27 November 2014


Name:CD4+ T Cells, donor1
Species:Human (Homo sapiens)
Library ID:CNhs10853
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage53 years old adult
sexmale
age53
cell typet cell, CD4+
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCD4T727
catalog number3H100-23-10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005494
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10853 CAGE DRX008176 DRR009048
Accession ID Hg19

Library idBAMCTSS
CNhs10853 DRZ000473 DRZ001858
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-Basophils0.339
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.139
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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-Whole0.144
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: CNhs10853

Jaspar motifP-value
MA0002.20.00226
MA0003.10.222
MA0004.10.945
MA0006.10.0677
MA0007.10.454
MA0009.10.0868
MA0014.10.961
MA0017.10.188
MA0018.24.65061e-9
MA0019.10.533
MA0024.10.869
MA0025.10.146
MA0027.10.933
MA0028.10.017
MA0029.10.404
MA0030.10.00766
MA0031.13.20978e-6
MA0035.20.209
MA0038.10.135
MA0039.20.584
MA0040.10.588
MA0041.10.279
MA0042.10.71
MA0043.17.59145e-4
MA0046.10.197
MA0047.20.139
MA0048.10.817
MA0050.19.26412e-6
MA0051.10.0182
MA0052.10.02
MA0055.10.957
MA0057.10.171
MA0058.10.924
MA0059.10.83
MA0060.10.366
MA0061.14.44245e-7
MA0062.26.78481e-11
MA0065.20.735
MA0066.10.601
MA0067.10.0114
MA0068.10.791
MA0069.10.86
MA0070.10.584
MA0071.10.72
MA0072.10.239
MA0073.10.905
MA0074.10.33
MA0076.10.00271
MA0077.10.0744
MA0078.10.931
MA0079.20.808
MA0080.22.57955e-9
MA0081.10.00984
MA0083.10.169
MA0084.10.257
MA0087.10.757
MA0088.10.76
MA0090.14.3739e-4
MA0091.10.164
MA0092.10.701
MA0093.10.979
MA0099.20.192
MA0100.10.631
MA0101.12.77728e-5
MA0102.20.968
MA0103.10.724
MA0104.20.278
MA0105.11.53562e-4
MA0106.10.0337
MA0107.16.3255e-5
MA0108.22.56528e-4
MA0111.10.439
MA0112.20.0595
MA0113.10.347
MA0114.10.221
MA0115.10.294
MA0116.10.233
MA0117.10.0371
MA0119.10.678
MA0122.10.879
MA0124.10.697
MA0125.10.0746
MA0131.10.064
MA0135.10.136
MA0136.14.08429e-16
MA0137.20.347
MA0138.20.0206
MA0139.10.762
MA0140.10.225
MA0141.10.0406
MA0142.10.122
MA0143.10.217
MA0144.10.44
MA0145.10.0164
MA0146.10.966
MA0147.10.336
MA0148.10.441
MA0149.10.817
MA0150.10.89
MA0152.10.0105
MA0153.10.211
MA0154.10.747
MA0155.10.166
MA0156.17.03042e-12
MA0157.16.82713e-5
MA0159.10.824
MA0160.10.406
MA0162.10.0745
MA0163.10.0533
MA0164.10.881
MA0258.10.514
MA0259.10.289



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: CNhs10853

Novel motifP-value
10.847
100.0173
1000.857
1010.148
1020.874
1030.459
1040.956
1050.532
1060.718
1070.00919
1080.458
1090.929
110.699
1100.429
1110.754
1120.708
1130.282
1140.963
1150.227
1160.154
1170.00911
1180.616
1190.181
120.715
1200.359
1210.485
1220.946
1231.38178e-5
1240.818
1250.501
1260.862
1270.415
1280.536
1290.416
130.723
1300.292
1310.567
1320.281
1330.712
1340.946
1350.245
1360.925
1370.0264
1380.658
1390.168
140.674
1400.386
1410.727
1420.321
1430.0874
1440.815
1450.729
1460.537
1470.0193
1480.455
1490.194
150.456
1500.715
1510.641
1520.229
1530.444
1540.127
1550.0544
1560.904
1570.588
1580.00457
1590.96
160.219
1600.0936
1610.652
1620.0226
1630.794
1640.171
1650.965
1660.293
1670.136
1680.562
1690.1
170.582
180.494
190.0235
20.129
200.178
210.723
220.188
230.43
240.55
250.218
260.848
270.654
280.401
290.161
30.445
300.039
310.462
320.00196
330.555
340.24
350.242
360.119
370.789
380.652
390.27
40.933
400.417
410.201
420.184
430.813
440.548
450.136
460.918
470.538
480.938
490.176
50.715
500.483
510.827
520.586
530.234
540.833
550.909
560.761
570.785
580.248
590.153
60.973
600.814
610.218
620.379
630.802
640.993
650.396
660.782
670.47
680.574
690.496
70.721
700.169
710.356
720.586
730.452
740.969
750.0929
760.073
770.00437
780.765
790.959
80.311
800.0727
810.979
820.604
830.771
840.19
850.539
860.208
870.291
880.964
890.00312
90.564
900.121
910.785
920.996
930.871
940.466
950.629
960.884
970.348
980.471
992.77473e-5



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: CNhs10853


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000031 (CD4-positive T cell 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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)

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