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FF:10060-101H6: 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 16:52, 29 March 2012


Name:thyroid, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethyroid
dev stage36 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA811069
catalog numberCat:RtHFN: Thyroid
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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.384
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-0.215
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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
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: CNhs11769

Jaspar motifP-value
MA0002.23.9344e-4
MA0003.10.245
MA0004.10.0484
MA0006.10.91
MA0007.10.244
MA0009.10.966
MA0014.10.868
MA0017.10.0651
MA0018.20.0136
MA0019.10.483
MA0024.10.67
MA0025.10.436
MA0027.10.72
MA0028.10.0886
MA0029.10.215
MA0030.10.991
MA0031.10.369
MA0035.20.00304
MA0038.10.591
MA0039.20.275
MA0040.10.335
MA0041.10.447
MA0042.10.935
MA0043.10.571
MA0046.10.0726
MA0047.20.806
MA0048.10.648
MA0050.10.0725
MA0051.10.0523
MA0052.18.73658e-5
MA0055.10.543
MA0057.10.926
MA0058.10.05
MA0059.10.0105
MA0060.10.0966
MA0061.11.19728e-4
MA0062.20.00321
MA0065.20.00244
MA0066.10.0128
MA0067.10.208
MA0068.10.999
MA0069.10.318
MA0070.10.992
MA0071.10.551
MA0072.10.196
MA0073.10.515
MA0074.10.684
MA0076.10.118
MA0077.10.995
MA0078.10.216
MA0079.20.533
MA0080.27.43616e-9
MA0081.10.0388
MA0083.10.708
MA0084.10.436
MA0087.10.971
MA0088.10.0289
MA0090.10.366
MA0091.10.0969
MA0092.10.21
MA0093.10.0582
MA0099.21.01314e-23
MA0100.10.522
MA0101.14.5531e-4
MA0102.20.00332
MA0103.10.526
MA0104.20.00242
MA0105.16.31508e-9
MA0106.10.0198
MA0107.11.56794e-4
MA0108.20.00102
MA0111.10.617
MA0112.20.0058
MA0113.10.743
MA0114.10.0509
MA0115.10.187
MA0116.14.20357e-5
MA0117.10.517
MA0119.10.968
MA0122.10.665
MA0124.10.336
MA0125.10.733
MA0131.10.631
MA0135.10.328
MA0136.11.14266e-10
MA0137.20.221
MA0138.20.58
MA0139.10.118
MA0140.10.00167
MA0141.10.153
MA0142.10.0121
MA0143.10.119
MA0144.10.288
MA0145.10.564
MA0146.10.189
MA0147.10.00127
MA0148.10.781
MA0149.10.158
MA0150.13.30756e-6
MA0152.10.138
MA0153.10.91
MA0154.19.71459e-4
MA0155.10.835
MA0156.11.73342e-7
MA0157.10.291
MA0159.10.0513
MA0160.10.07
MA0162.10.213
MA0163.18.03937e-9
MA0164.10.446
MA0258.10.0503
MA0259.10.164



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: CNhs11769

Novel motifP-value
10.118
100.12
1000.72
1010.853
1020.808
1030.00932
1040.53
1050.94
1060.128
1070.533
1080.946
1090.00159
110.0385
1100.141
1110.476
1120.955
1130.0479
1140.0562
1150.998
1160.991
1170.0327
1180.162
1190.549
120.493
1200.189
1210.917
1220.242
1230.23
1240.31
1250.486
1260.522
1270.19
1280.433
1290.533
130.332
1300.159
1310.734
1320.05
1330.397
1340.855
1350.839
1360.318
1370.275
1380.775
1390.611
140.916
1400.6
1410.928
1420.151
1430.00699
1440.709
1450.652
1460.156
1470.774
1480.101
1490.666
150.121
1500.258
1510.53
1520.597
1530.953
1540.833
1550.474
1560.742
1570.441
1580.295
1590.126
160.136
1600.354
1610.42
1620.619
1630.0305
1640.953
1650.988
1660.979
1670.287
1680.397
1690.0476
170.0812
180.00334
190.575
20.968
200.55
210.706
220.211
230.232
240.116
250.585
260.0788
270.169
280.675
290.073
30.116
300.507
310.534
320.977
330.275
340.799
350.272
360.0303
370.0727
380.408
390.734
40.471
400.0742
410.0634
420.128
430.0378
440.652
450.646
460.0457
470.0463
480.0998
490.106
50.333
500.933
510.28
520.719
530.938
540.285
550.706
560.244
570.613
580.547
590.0956
60.8
600.437
610.217
620.159
630.584
640.143
650.258
660.0382
670.66
680.949
690.804
70.585
700.0562
710.0414
720.1
730.182
740.692
750.053
760.648
770.341
780.636
790.938
80.0648
800.118
810.29
820.527
830.349
840.851
850.442
860.252
871.45721e-4
880.91
890.398
90.201
900.201
910.378
920.818
930.815
940.0437
950.0104
960.319
970.884
980.71
990.79



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: CNhs11769


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)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002046 (thyroid gland)
0002050 (embryonic structure)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0003091 (thyroid primordium)
0003104 (mesenchyme)
0004117 (pharyngeal pouch)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006562 (pharynx)
0007026 (primitive gut)
0007123 (pharyngeal pouch 2)
0007689 (thyroid diverticulum)
0007690 (early pharyngeal endoderm)
0008814 (pharyngeal arch system)
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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