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FF:11786-124B4: 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 17:31, 29 March 2012


Name:CD4+CD25-CD45RA- memory conventional T cells, donor1
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
age25
cell typeT cell
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number4
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-Basophils0.566
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.165
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.221
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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-Whole0.332
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: CNhs13239

Jaspar motifP-value
MA0002.23.34367e-7
MA0003.10.633
MA0004.10.87
MA0006.10.0806
MA0007.10.741
MA0009.10.0858
MA0014.10.643
MA0017.10.784
MA0018.23.66639e-10
MA0019.10.275
MA0024.10.647
MA0025.10.0274
MA0027.10.551
MA0028.11.37653e-5
MA0029.10.363
MA0030.11.77628e-4
MA0031.16.72121e-6
MA0035.20.121
MA0038.10.315
MA0039.20.729
MA0040.10.593
MA0041.10.843
MA0042.10.622
MA0043.10.00151
MA0046.10.363
MA0047.20.0258
MA0048.10.784
MA0050.13.04223e-7
MA0051.10.00293
MA0052.10.0262
MA0055.10.767
MA0057.10.389
MA0058.10.638
MA0059.10.7
MA0060.10.883
MA0061.17.51223e-5
MA0062.27.48837e-21
MA0065.20.593
MA0066.10.385
MA0067.10.00163
MA0068.10.732
MA0069.10.781
MA0070.10.872
MA0071.10.904
MA0072.10.00573
MA0073.10.874
MA0074.10.483
MA0076.19.61873e-8
MA0077.10.0244
MA0078.10.661
MA0079.20.703
MA0080.23.43991e-12
MA0081.10.00591
MA0083.10.166
MA0084.10.44
MA0087.10.406
MA0088.10.526
MA0090.11.38726e-4
MA0091.10.36
MA0092.10.759
MA0093.10.92
MA0099.20.0766
MA0100.10.75
MA0101.10.0275
MA0102.20.967
MA0103.10.643
MA0104.20.061
MA0105.14.5702e-6
MA0106.10.0312
MA0107.10.057
MA0108.23.76511e-4
MA0111.10.658
MA0112.20.538
MA0113.10.833
MA0114.10.74
MA0115.10.427
MA0116.10.00467
MA0117.10.0123
MA0119.10.101
MA0122.10.456
MA0124.10.214
MA0125.10.186
MA0131.10.098
MA0135.10.764
MA0136.15.78667e-25
MA0137.20.764
MA0138.20.132
MA0139.10.108
MA0140.10.0975
MA0141.10.334
MA0142.10.348
MA0143.10.451
MA0144.10.812
MA0145.10.0441
MA0146.10.728
MA0147.10.101
MA0148.10.117
MA0149.10.294
MA0150.10.579
MA0152.10.00934
MA0153.10.349
MA0154.10.242
MA0155.10.263
MA0156.12.30843e-23
MA0157.11.447e-4
MA0159.10.489
MA0160.10.9
MA0162.10.383
MA0163.12.77839e-4
MA0164.10.84
MA0258.10.82
MA0259.10.187



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: CNhs13239

Novel motifP-value
10.713
100.0255
1000.96
1010.439
1020.904
1030.543
1040.656
1050.159
1060.733
1070.00202
1080.468
1090.211
110.447
1100.969
1110.549
1120.931
1130.381
1140.923
1150.391
1160.0868
1170.00282
1180.488
1190.169
120.593
1200.726
1210.821
1220.577
1230.0844
1240.691
1250.537
1260.405
1270.977
1280.57
1290.884
130.715
1300.626
1310.524
1320.228
1330.713
1340.747
1350.943
1360.9
1370.0375
1380.752
1390.159
140.68
1400.315
1410.887
1420.626
1430.00125
1440.79
1450.467
1460.86
1470.0152
1480.295
1490.532
150.253
1500.81
1510.608
1520.557
1530.926
1540.518
1550.0245
1560.588
1570.217
1580.02
1590.233
160.479
1600.12
1610.563
1620.0138
1630.388
1640.18
1650.644
1660.294
1670.346
1680.471
1690.145
170.707
180.89
190.032
20.308
200.286
210.843
220.348
230.54
240.7
250.105
260.989
270.67
280.531
290.0316
30.435
300.154
310.723
320.0282
330.191
340.396
350.302
360.0355
370.257
380.712
390.194
40.557
400.798
410.105
420.192
430.645
440.882
450.266
460.703
470.389
480.61
490.277
50.475
500.415
510.808
520.385
530.616
540.995
550.963
560.799
570.901
580.155
590.5
60.642
600.707
610.15
620.205
630.734
640.741
650.654
660.733
670.681
680.74
690.805
70.477
700.191
710.108
720.152
730.509
740.986
750.026
760.174
770.00821
780.575
790.472
80.415
800.00163
810.815
820.347
830.461
840.585
850.629
860.0737
870.845
880.892
890.0342
90.985
900.159
910.998
920.939
930.513
940.28
950.00457
960.594
970.455
980.346
993.7156e-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: CNhs13239


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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