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FF:11307-117C2: 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 17:03, 29 March 2012


Name:CD8+ 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 stage57 years old adult
sexmale
age57
cell typet cell, CD8+
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCD8T726
catalog number3H100-26-10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Basophils0.186
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0559
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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-Whole0.723
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: CNhs11956

Jaspar motifP-value
MA0002.23.74238e-4
MA0003.10.335
MA0004.10.813
MA0006.10.333
MA0007.10.377
MA0009.10.0289
MA0014.10.647
MA0017.10.0966
MA0018.26.87486e-9
MA0019.10.718
MA0024.10.685
MA0025.10.268
MA0027.10.667
MA0028.10.153
MA0029.10.617
MA0030.10.0203
MA0031.13.20367e-5
MA0035.20.406
MA0038.10.016
MA0039.20.195
MA0040.10.609
MA0041.10.225
MA0042.10.594
MA0043.10.00373
MA0046.10.0339
MA0047.20.67
MA0048.10.64
MA0050.12.60542e-5
MA0051.10.0907
MA0052.10.0289
MA0055.10.583
MA0057.10.205
MA0058.10.746
MA0059.10.783
MA0060.10.0187
MA0061.11.36991e-10
MA0062.21.45051e-7
MA0065.20.881
MA0066.10.661
MA0067.10.00378
MA0068.10.9
MA0069.10.616
MA0070.10.413
MA0071.10.772
MA0072.10.0797
MA0073.10.531
MA0074.10.963
MA0076.10.0822
MA0077.10.0899
MA0078.10.974
MA0079.20.773
MA0080.22.18565e-8
MA0081.10.0425
MA0083.10.314
MA0084.10.244
MA0087.10.548
MA0088.10.197
MA0090.12.68744e-4
MA0091.10.279
MA0092.10.825
MA0093.10.713
MA0099.20.634
MA0100.10.905
MA0101.18.27359e-7
MA0102.20.74
MA0103.10.937
MA0104.20.715
MA0105.14.37854e-8
MA0106.10.0722
MA0107.12.31565e-6
MA0108.21.03725e-4
MA0111.10.408
MA0112.20.288
MA0113.10.487
MA0114.10.18
MA0115.10.244
MA0116.10.114
MA0117.10.0137
MA0119.10.268
MA0122.10.706
MA0124.10.0688
MA0125.10.068
MA0131.10.0812
MA0135.10.178
MA0136.19.32993e-12
MA0137.20.0313
MA0138.20.0593
MA0139.10.841
MA0140.10.672
MA0141.10.186
MA0142.10.124
MA0143.10.206
MA0144.10.192
MA0145.10.0234
MA0146.10.767
MA0147.10.638
MA0148.11
MA0149.10.61
MA0150.10.286
MA0152.10.00132
MA0153.10.144
MA0154.10.779
MA0155.10.182
MA0156.12.59997e-7
MA0157.10.00238
MA0159.10.989
MA0160.10.651
MA0162.10.355
MA0163.10.0205
MA0164.10.592
MA0258.10.964
MA0259.10.767



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: CNhs11956

Novel motifP-value
10.954
100.00619
1000.735
1010.186
1020.774
1030.28
1040.929
1050.91
1060.124
1070.0632
1080.749
1090.986
110.74
1100.36
1110.476
1120.802
1130.26
1140.701
1150.566
1160.192
1170.0079
1180.537
1190.585
120.78
1200.253
1210.601
1220.727
1233.68154e-6
1240.972
1250.901
1260.702
1270.397
1280.772
1290.155
130.672
1300.146
1310.228
1320.284
1330.816
1340.676
1350.185
1360.739
1370.0626
1380.69
1390.102
140.492
1400.799
1410.948
1420.326
1430.0338
1440.997
1450.499
1460.361
1470.0418
1480.259
1490.216
150.456
1500.828
1510.496
1520.917
1530.404
1540.0813
1550.0925
1560.909
1570.726
1580.0109
1590.881
160.229
1600.0671
1610.676
1620.0589
1630.651
1640.055
1650.866
1660.544
1670.121
1680.41
1690.282
170.548
180.762
190.0616
20.188
200.142
210.999
220.146
230.732
240.379
250.238
260.996
270.461
280.308
290.0953
30.588
300.0358
310.564
320.0373
330.593
340.251
350.342
360.187
370.359
380.598
390.509
40.8
400.803
410.237
420.4
430.618
440.605
450.101
460.912
470.763
480.941
490.185
50.832
500.435
510.977
520.958
530.243
540.945
550.847
560.726
570.977
580.21
590.219
60.909
600.607
610.282
620.369
630.827
640.986
650.534
660.318
670.475
680.851
690.873
70.842
700.2
710.265
720.594
730.498
740.545
750.0558
760.0946
770.00272
780.724
790.586
80.302
800.173
810.906
820.667
830.782
840.115
850.665
860.0384
870.957
880.947
890.00157
90.579
900.664
910.791
920.909
930.958
940.325
950.203
960.792
970.214
980.529
998.09635e-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: CNhs11956


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)
0000625 (CD8-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)
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)

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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