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FF:11306-117C1: 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 17:02, 29 March 2012


Name:CD4+ 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, CD4+
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCD4T726
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-Basophils0.338
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0635
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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-Whole0.144
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 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: CNhs11955

Jaspar motifP-value
MA0002.20.00301
MA0003.10.257
MA0004.10.915
MA0006.10.151
MA0007.10.857
MA0009.10.0719
MA0014.10.734
MA0017.10.185
MA0018.21.92494e-7
MA0019.10.442
MA0024.10.678
MA0025.10.312
MA0027.10.937
MA0028.10.335
MA0029.10.245
MA0030.10.0789
MA0031.11.72024e-4
MA0035.20.768
MA0038.10.0135
MA0039.20.225
MA0040.10.536
MA0041.10.229
MA0042.10.552
MA0043.10.0341
MA0046.10.0501
MA0047.20.646
MA0048.10.748
MA0050.10.00179
MA0051.10.219
MA0052.10.0342
MA0055.10.755
MA0057.10.186
MA0058.10.801
MA0059.10.894
MA0060.10.00533
MA0061.15.48624e-9
MA0062.24.19552e-5
MA0065.20.921
MA0066.10.929
MA0067.10.0232
MA0068.10.987
MA0069.10.583
MA0070.10.405
MA0071.10.969
MA0072.10.322
MA0073.10.805
MA0074.10.971
MA0076.10.2
MA0077.10.0643
MA0078.10.964
MA0079.20.544
MA0080.26.48188e-7
MA0081.10.0655
MA0083.10.175
MA0084.10.594
MA0087.10.451
MA0088.10.427
MA0090.17.90209e-4
MA0091.10.253
MA0092.10.919
MA0093.10.762
MA0099.20.0947
MA0100.10.864
MA0101.11.16697e-5
MA0102.20.815
MA0103.10.459
MA0104.20.42
MA0105.11.6208e-7
MA0106.10.0669
MA0107.14.26221e-5
MA0108.22.47207e-5
MA0111.10.304
MA0112.20.433
MA0113.10.436
MA0114.10.351
MA0115.10.167
MA0116.10.0507
MA0117.10.0514
MA0119.10.903
MA0122.10.665
MA0124.10.16
MA0125.10.0992
MA0131.10.159
MA0135.10.102
MA0136.12.34571e-9
MA0137.20.0348
MA0138.20.0686
MA0139.10.854
MA0140.10.98
MA0141.10.232
MA0142.10.131
MA0143.10.194
MA0144.10.166
MA0145.10.0142
MA0146.10.762
MA0147.10.373
MA0148.10.936
MA0149.10.474
MA0150.10.645
MA0152.10.00542
MA0153.10.132
MA0154.10.805
MA0155.10.265
MA0156.11.24132e-5
MA0157.16.83819e-4
MA0159.10.934
MA0160.10.498
MA0162.10.241
MA0163.10.00518
MA0164.10.541
MA0258.10.686
MA0259.10.429



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: CNhs11955

Novel motifP-value
10.638
100.00777
1000.456
1010.114
1020.784
1030.294
1040.899
1050.852
1060.22
1070.143
1080.966
1090.795
110.487
1100.596
1110.291
1120.897
1130.252
1140.619
1150.778
1160.473
1170.00574
1180.386
1190.812
120.703
1200.432
1210.798
1220.604
1237.16985e-8
1240.769
1250.911
1260.936
1270.254
1280.998
1290.433
130.562
1300.165
1310.796
1320.342
1330.673
1340.808
1350.271
1360.936
1370.0371
1380.476
1390.0893
140.595
1400.323
1410.928
1420.333
1430.147
1440.845
1450.907
1460.342
1470.0608
1480.216
1490.235
150.339
1500.96
1510.49
1520.524
1530.386
1540.0708
1550.112
1560.749
1570.757
1580.00869
1590.895
160.307
1600.237
1610.468
1620.0942
1630.874
1640.0312
1650.936
1660.404
1670.0744
1680.412
1690.28
170.66
180.59
190.0802
20.182
200.144
210.59
220.193
230.764
240.387
250.196
260.592
270.6
280.394
290.0568
30.337
300.0178
310.523
320.0454
330.461
340.203
350.137
360.141
370.453
380.832
390.54
40.732
400.651
410.453
420.211
430.528
440.861
450.109
460.651
470.443
480.746
490.0929
50.731
500.459
510.931
520.79
530.19
540.885
550.959
560.825
570.583
580.196
590.28
60.663
600.552
610.226
620.249
630.908
640.749
650.644
660.17
670.567
680.811
690.684
70.772
700.0918
710.169
720.586
730.928
740.758
750.0215
760.0368
770.00714
780.582
790.598
80.588
800.244
810.741
820.449
830.901
840.0637
850.891
860.0808
870.449
880.897
890.00465
90.445
900.262
910.467
920.616
930.377
940.447
950.278
960.856
970.279
980.274
991.05599e-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: CNhs11955


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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