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FF:11382-118B5: 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 17:05, 29 March 2012


Name:CD4+ T Cells, donor3
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 stage26 years old adult
sexfemale
age26
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 numberCD4T734
catalog number3H100-23-10
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-Basophils0.422
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0203
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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-Whole0.15
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: CNhs11998

Jaspar motifP-value
MA0002.24.33473e-4
MA0003.10.276
MA0004.10.955
MA0006.10.111
MA0007.10.644
MA0009.10.042
MA0014.10.907
MA0017.10.157
MA0018.26.19938e-11
MA0019.10.899
MA0024.10.76
MA0025.10.0314
MA0027.10.924
MA0028.10.0907
MA0029.10.216
MA0030.10.0112
MA0031.12.54189e-4
MA0035.20.365
MA0038.10.0471
MA0039.20.783
MA0040.10.658
MA0041.10.221
MA0042.10.677
MA0043.15.83864e-5
MA0046.10.0732
MA0047.20.406
MA0048.10.903
MA0050.11.49341e-5
MA0051.10.0383
MA0052.10.0728
MA0055.10.814
MA0057.10.228
MA0058.10.995
MA0059.10.798
MA0060.10.317
MA0061.16.26596e-7
MA0062.21.71693e-9
MA0065.20.644
MA0066.10.883
MA0067.17.16197e-4
MA0068.10.713
MA0069.10.882
MA0070.10.655
MA0071.10.482
MA0072.10.174
MA0073.10.767
MA0074.10.762
MA0076.10.0299
MA0077.10.0344
MA0078.10.986
MA0079.20.887
MA0080.22.98949e-10
MA0081.10.00744
MA0083.10.886
MA0084.10.528
MA0087.10.369
MA0088.10.179
MA0090.11.6737e-4
MA0091.10.208
MA0092.10.607
MA0093.10.926
MA0099.20.154
MA0100.10.99
MA0101.12.06805e-4
MA0102.20.883
MA0103.10.778
MA0104.20.363
MA0105.11.03783e-5
MA0106.10.0231
MA0107.12.37832e-4
MA0108.20.00742
MA0111.10.338
MA0112.20.0825
MA0113.10.282
MA0114.10.17
MA0115.10.163
MA0116.10.102
MA0117.10.0148
MA0119.10.388
MA0122.10.934
MA0124.10.152
MA0125.10.207
MA0131.10.0679
MA0135.10.372
MA0136.12.21623e-16
MA0137.20.193
MA0138.20.0238
MA0139.10.901
MA0140.10.42
MA0141.10.0575
MA0142.10.101
MA0143.10.181
MA0144.10.371
MA0145.10.00955
MA0146.10.853
MA0147.10.365
MA0148.10.96
MA0149.10.612
MA0150.10.398
MA0152.10.00195
MA0153.10.0921
MA0154.10.702
MA0155.10.135
MA0156.13.56145e-10
MA0157.10.00342
MA0159.10.794
MA0160.10.424
MA0162.10.104
MA0163.10.0374
MA0164.10.762
MA0258.10.503
MA0259.10.291



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: CNhs11998

Novel motifP-value
10.96
100.00942
1000.639
1010.384
1020.839
1030.326
1040.945
1050.943
1060.276
1070.0114
1080.767
1090.958
110.768
1100.433
1110.853
1120.909
1130.387
1140.944
1150.664
1160.143
1170.00816
1180.485
1190.315
120.855
1200.473
1210.559
1220.902
1231.8901e-4
1240.601
1250.78
1260.914
1270.62
1280.639
1290.413
130.761
1300.172
1310.679
1320.232
1330.878
1340.89
1350.293
1360.706
1370.0289
1380.624
1390.0987
140.811
1400.381
1410.888
1420.383
1430.0431
1440.874
1450.367
1460.239
1470.0312
1480.58
1490.175
150.472
1500.975
1510.643
1520.694
1530.665
1540.159
1550.0554
1560.807
1570.669
1580.00492
1590.804
160.274
1600.0321
1610.659
1620.0135
1630.732
1640.074
1650.852
1660.257
1670.147
1680.43
1690.109
170.579
180.658
190.0261
20.1
200.157
210.949
220.164
230.863
240.452
250.184
260.984
270.676
280.5
290.0676
30.692
300.049
310.497
320.00673
330.415
340.21
350.517
360.142
370.594
380.519
390.295
40.996
400.529
410.192
420.38
430.893
440.864
450.0857
460.988
470.61
480.973
490.379
50.898
500.398
510.768
520.729
530.448
540.705
550.564
560.675
570.879
580.245
590.134
60.994
600.68
610.347
620.317
630.672
640.97
650.497
660.438
670.457
680.86
690.606
70.803
700.178
710.28
720.61
730.821
740.533
750.0617
760.177
770.0015
780.868
790.635
80.295
800.0822
810.966
820.564
830.709
840.122
850.879
860.0769
870.629
880.936
890.00176
90.663
900.411
910.777
920.946
930.842
940.505
950.209
960.953
970.379
980.424
991.57038e-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: CNhs11998


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)
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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