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FF:11917-125G9: 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 17:39, 29 March 2012


Name:CD4+CD25-CD45RA+ naive conventional T cells expanded, 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 number61-62
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-Basophils0.106
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0837
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-lymphoma0.285
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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
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: CNhs13814

Jaspar motifP-value
MA0002.24.95159e-6
MA0003.10.903
MA0004.10.862
MA0006.10.447
MA0007.10.874
MA0009.10.541
MA0014.10.687
MA0017.10.335
MA0018.20.596
MA0019.10.18
MA0024.10.0512
MA0025.10.129
MA0027.10.468
MA0028.11.49964e-4
MA0029.10.562
MA0030.10.274
MA0031.10.765
MA0035.20.21
MA0038.10.063
MA0039.20.603
MA0040.10.236
MA0041.10.197
MA0042.10.437
MA0043.10.107
MA0046.10.0454
MA0047.20.933
MA0048.10.675
MA0050.13.31302e-6
MA0051.10.0342
MA0052.10.0124
MA0055.10.518
MA0057.10.855
MA0058.10.964
MA0059.10.282
MA0060.10.987
MA0061.10.0583
MA0062.28.86034e-12
MA0065.20.0432
MA0066.10.488
MA0067.10.885
MA0068.10.916
MA0069.10.856
MA0070.10.509
MA0071.10.592
MA0072.10.928
MA0073.10.773
MA0074.10.777
MA0076.16.07993e-6
MA0077.10.0501
MA0078.10.737
MA0079.20.393
MA0080.21.20144e-10
MA0081.10.0484
MA0083.10.041
MA0084.10.667
MA0087.10.369
MA0088.10.0633
MA0090.16.2363e-4
MA0091.10.954
MA0092.10.635
MA0093.10.799
MA0099.25.22055e-6
MA0100.10.704
MA0101.10.817
MA0102.20.365
MA0103.10.0753
MA0104.20.19
MA0105.12.1504e-5
MA0106.10.902
MA0107.10.385
MA0108.21.09637e-10
MA0111.10.0663
MA0112.20.128
MA0113.10.849
MA0114.10.251
MA0115.10.608
MA0116.19.14898e-5
MA0117.10.858
MA0119.10.751
MA0122.10.829
MA0124.10.379
MA0125.10.343
MA0131.10.2
MA0135.10.029
MA0136.17.38462e-19
MA0137.20.711
MA0138.20.438
MA0139.10.0204
MA0140.10.334
MA0141.10.562
MA0142.10.207
MA0143.10.099
MA0144.10.944
MA0145.10.43
MA0146.10.0892
MA0147.10.157
MA0148.10.532
MA0149.10.0622
MA0150.10.161
MA0152.10.0192
MA0153.10.0937
MA0154.10.0369
MA0155.10.709
MA0156.11.36055e-14
MA0157.10.364
MA0159.10.47
MA0160.10.639
MA0162.10.729
MA0163.13.68479e-12
MA0164.10.826
MA0258.10.0358
MA0259.10.412



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: CNhs13814

Novel motifP-value
10.0806
100.00508
1000.469
1010.0952
1020.473
1030.799
1040.589
1050.255
1060.41
1070.462
1080.846
1090.108
110.0398
1100.395
1110.27
1120.285
1130.318
1140.439
1150.27
1160.515
1170.00407
1180.357
1190.551
120.581
1200.782
1210.964
1220.669
1236.73911e-7
1240.334
1250.948
1260.463
1270.725
1280.751
1290.339
130.469
1300.659
1310.62
1320.61
1330.364
1340.668
1350.837
1360.721
1370.243
1380.317
1390.194
140.491
1400.019
1410.539
1420.701
1430.00451
1440.442
1450.135
1460.662
1470.216
1480.0613
1490.868
150.273
1500.603
1510.542
1520.339
1530.932
1540.496
1550.0623
1560.851
1570.19
1580.22
1590.505
160.729
1600.287
1610.168
1620.447
1630.287
1640.0628
1650.642
1660.78
1670.139
1680.628
1690.344
170.915
180.981
190.645
20.912
200.522
210.168
220.834
230.504
240.932
250.0669
260.0335
270.239
280.712
290.0148
30.0389
300.08
310.991
320.526
330.643
340.938
350.224
360.0188
370.297
380.544
390.36
40.968
400.289
410.74
420.0931
430.397
440.502
450.412
460.11
470.0163
480.0469
490.0982
50.795
501
510.716
520.347
530.117
540.794
550.595
560.4
570.177
580.0814
590.422
60.394
600.496
610.128
620.0538
630.357
640.154
650.787
660.672
670.515
680.958
690.986
70.238
700.111
710.0308
720.17
730.546
740.538
750.0125
760.195
770.41
780.0155
790.499
80.432
800.248
810.343
820.0926
830.407
840.0336
850.702
860.248
870.663
880.796
890.237
90.871
900.049
910.274
920.451
930.309
940.144
950.0121
960.176
970.239
980.402
990.367



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: CNhs13814


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)
0000813 (memory T cell)
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)
0000896 (activated CD4-positive, alpha-beta T cell)
0000897 (CD4-positive, alpha-beta memory 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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