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FF:10027-101D9: 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 16:27, 29 March 2012


Name:thymus, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethymus
dev stage0.5,0.5,0.83 years old infant
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -18
catalog numberCat:AM6000 Lot:0910061 -18
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-Basophils0.0272
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.17
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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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-Whole0.0528
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: CNhs10633

Jaspar motifP-value
MA0002.23.54087e-4
MA0003.10.889
MA0004.10.359
MA0006.10.808
MA0007.10.36
MA0009.10.677
MA0014.10.351
MA0017.10.72
MA0018.20.674
MA0019.10.142
MA0024.11.27421e-6
MA0025.10.17
MA0027.10.56
MA0028.11.33366e-4
MA0029.10.866
MA0030.10.267
MA0031.10.0296
MA0035.20.252
MA0038.10.427
MA0039.20.416
MA0040.10.615
MA0041.10.413
MA0042.10.465
MA0043.10.113
MA0046.10.732
MA0047.20.274
MA0048.10.00149
MA0050.12.40014e-6
MA0051.10.0174
MA0052.10.184
MA0055.10.00366
MA0057.10.38
MA0058.10.455
MA0059.10.0658
MA0060.17.85189e-8
MA0061.10.462
MA0062.28.50662e-16
MA0065.20.486
MA0066.10.727
MA0067.10.173
MA0068.10.0341
MA0069.10.668
MA0070.10.314
MA0071.10.198
MA0072.10.838
MA0073.10.21
MA0074.10.052
MA0076.15.32292e-9
MA0077.10.859
MA0078.10.688
MA0079.20.361
MA0080.26.92855e-11
MA0081.10.014
MA0083.10.00432
MA0084.10.71
MA0087.10.804
MA0088.10.351
MA0090.14.44909e-4
MA0091.10.37
MA0092.10.649
MA0093.10.407
MA0099.29.54013e-16
MA0100.11.59558e-4
MA0101.10.693
MA0102.20.276
MA0103.14.43103e-4
MA0104.20.955
MA0105.10.725
MA0106.10.0555
MA0107.10.928
MA0108.20.262
MA0111.10.494
MA0112.20.0181
MA0113.10.673
MA0114.10.187
MA0115.10.869
MA0116.10.382
MA0117.10.644
MA0119.10.0166
MA0122.10.344
MA0124.10.308
MA0125.10.494
MA0131.10.427
MA0135.10.546
MA0136.11.27867e-14
MA0137.20.0269
MA0138.20.708
MA0139.10.268
MA0140.10.845
MA0141.10.00217
MA0142.10.587
MA0143.10.1
MA0144.10.345
MA0145.10.102
MA0146.10.242
MA0147.10.681
MA0148.10.952
MA0149.10.201
MA0150.11.70295e-5
MA0152.10.0595
MA0153.10.381
MA0154.10.548
MA0155.10.518
MA0156.13.23827e-17
MA0157.10.152
MA0159.10.384
MA0160.10.142
MA0162.10.245
MA0163.10.823
MA0164.10.448
MA0258.10.105
MA0259.10.703



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: CNhs10633

Novel motifP-value
10.417
100.805
1000.174
1010.978
1020.837
1030.612
1040.804
1050.568
1060.087
1070.179
1080.243
1090.376
110.782
1100.249
1110.254
1120.8
1130.585
1140.00672
1150.508
1160.336
1170.225
1180.136
1190.239
120.58
1200.82
1210.11
1220.336
1230.199
1240.228
1250.349
1260.664
1270.36
1280.464
1290.35
130.181
1300.00603
1310.925
1320.842
1330.98
1340.853
1350.047
1360.501
1370.194
1380.533
1390.331
140.687
1400.0406
1410.522
1420.238
1430.201
1440.786
1450.508
1460.138
1470.115
1480.88
1490.303
150.621
1500.699
1510.834
1520.0377
1530.909
1540.353
1550.115
1560.251
1570.0393
1580.621
1590.102
160.392
1600.628
1610.521
1620.387
1630.219
1640.104
1650.898
1660.387
1670.425
1680.093
1690.02
170.284
180.183
190.0127
20.203
200.0318
210.948
220.13
230.182
240.963
250.247
260.859
270.018
280.823
290.599
30.765
300.361
310.392
320.00905
330.497
340.91
350.581
360.471
370.0728
380.78
390.158
40.852
400.172
410.892
420.559
430.592
440.35
450.729
460.571
470.893
480.633
490.524
50.413
500.809
510.97
520.311
530.978
540.498
550.805
560.976
570.0576
580.325
590.59
60.47
600.57
610.208
620.379
630.507
640.746
650.433
660.683
670.24
680.44
690.599
70.74
700.107
710.297
720.0289
730.00672
740.713
750.809
760.12
770.0938
780.862
790.339
80.0638
808.08091e-5
810.706
820.799
830.791
840.334
850.0207
860.505
870.527
880.117
890.274
90.368
900.505
910.925
920.251
930.703
940.902
950.532
960.1
970.537
980.193
990.242



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: CNhs10633


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

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)
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)
0007023 (adult organism)
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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