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FF:11909-125G1: 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 17:37, 29 March 2012


Name:CD4+CD25-CD45RA- memory conventional 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 stageNA
sexmale
age23
cell typeT cell
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number39-40
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-Basophils0.515
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.131
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.401
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: CNhs13539

Jaspar motifP-value
MA0002.26.85667e-7
MA0003.10.47
MA0004.10.719
MA0006.10.135
MA0007.10.726
MA0009.10.0929
MA0014.10.993
MA0017.10.926
MA0018.23.47563e-6
MA0019.10.75
MA0024.10.725
MA0025.10.473
MA0027.10.859
MA0028.12.48867e-4
MA0029.10.149
MA0030.10.00465
MA0031.11.41627e-4
MA0035.20.226
MA0038.10.0377
MA0039.20.469
MA0040.10.623
MA0041.10.59
MA0042.10.739
MA0043.10.0377
MA0046.10.102
MA0047.20.0505
MA0048.10.756
MA0050.11.93587e-8
MA0051.10.00131
MA0052.10.00503
MA0055.10.693
MA0057.10.615
MA0058.10.711
MA0059.10.66
MA0060.10.0266
MA0061.10.00139
MA0062.22.87872e-15
MA0065.20.314
MA0066.10.212
MA0067.10.0285
MA0068.10.202
MA0069.10.903
MA0070.10.432
MA0071.10.699
MA0072.10.166
MA0073.10.942
MA0074.10.729
MA0076.13.72409e-6
MA0077.10.00719
MA0078.10.78
MA0079.20.327
MA0080.23.14537e-11
MA0081.10.0159
MA0083.10.0399
MA0084.10.358
MA0087.10.626
MA0088.10.397
MA0090.13.53184e-4
MA0091.10.652
MA0092.10.982
MA0093.10.597
MA0099.20.00285
MA0100.10.421
MA0101.10.286
MA0102.20.958
MA0103.10.346
MA0104.20.154
MA0105.12.4241e-6
MA0106.10.198
MA0107.10.403
MA0108.21.52826e-9
MA0111.10.3
MA0112.20.671
MA0113.10.65
MA0114.10.96
MA0115.10.454
MA0116.15.05178e-4
MA0117.10.0659
MA0119.10.672
MA0122.10.546
MA0124.10.406
MA0125.10.151
MA0131.10.139
MA0135.10.102
MA0136.11.27146e-22
MA0137.20.991
MA0138.20.292
MA0139.10.0437
MA0140.10.127
MA0141.10.326
MA0142.10.368
MA0143.10.35
MA0144.10.921
MA0145.10.194
MA0146.10.958
MA0147.10.114
MA0148.10.173
MA0149.10.242
MA0150.10.665
MA0152.10.0149
MA0153.10.219
MA0154.10.111
MA0155.10.271
MA0156.13.41286e-20
MA0157.10.00101
MA0159.10.427
MA0160.10.714
MA0162.10.635
MA0163.14.75593e-6
MA0164.10.966
MA0258.10.665
MA0259.10.262



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: CNhs13539

Novel motifP-value
10.22
100.00832
1000.822
1010.137
1020.889
1030.295
1040.961
1050.551
1060.713
1070.0147
1080.597
1090.343
110.256
1100.939
1110.688
1120.638
1130.214
1140.431
1150.313
1160.333
1170.00446
1180.28
1190.588
120.829
1200.672
1210.873
1220.92
1230.0081
1240.64
1250.861
1260.474
1270.9
1280.733
1290.969
130.456
1300.335
1310.725
1320.269
1330.985
1340.62
1350.629
1360.758
1370.0397
1380.34
1390.044
140.601
1400.0945
1410.405
1420.644
1430.00272
1440.819
1450.684
1460.851
1470.0224
1480.0854
1490.468
150.112
1500.668
1510.751
1520.19
1530.49
1540.38
1550.0609
1560.982
1570.267
1580.00916
1590.617
160.743
1600.387
1610.874
1620.0826
1630.518
1640.0933
1650.212
1660.599
1670.133
1680.483
1690.461
170.67
180.984
190.162
20.494
200.449
210.766
220.422
230.58
240.766
250.0635
260.654
270.512
280.483
290.0109
30.169
300.12
310.742
320.0726
330.247
340.324
350.127
360.0374
370.28
380.828
390.247
40.773
400.836
410.212
420.0915
430.478
440.64
450.279
460.374
470.221
480.428
490.136
50.31
500.402
510.817
520.321
530.543
540.905
550.56
560.996
570.679
580.121
590.835
60.921
600.634
610.144
620.0972
630.898
640.507
650.701
660.56
670.971
680.896
690.813
70.303
700.0589
710.0372
720.1
730.972
740.514
750.0238
760.113
770.0272
780.594
790.958
80.917
800.0152
810.396
820.16
830.95
840.885
850.795
860.175
870.341
880.873
890.12
90.786
900.0211
910.526
920.477
930.371
940.146
950.266
960.174
970.39
980.22
998.87521e-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: CNhs13539


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)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000810 (CD4-positive, alpha-beta thymocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)
0000898 (naive T 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)
0002425 (early T lineage precursor)
0002427 (resting double-positive thymocyte)
0002428 (double-positive blast)
0002429 (CD69-positive double-positive thymocyte)
0002431 (CD4-positive, CD8-intermediate double-positive thymocyte)
0002432 (CD24-positive, CD4 single-positive thymocyte)
0002433 (CD69-positive, CD4-positive single-positive thymocyte)
0002436 (mature CD4 single-positive thymocyte)
0002489 (double negative thymocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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