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FF:10028-101E1: 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 16:28, 29 March 2012


Name:thyroid, 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
tissuethyroid
dev stage67,68,78 years old adult
sexmixed
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 -19
catalog numberCat:AM6000 Lot:0910061 -19
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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.119
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-0.394
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.0268
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: CNhs10634

Jaspar motifP-value
MA0002.20.00522
MA0003.10.56
MA0004.10.365
MA0006.10.362
MA0007.10.76
MA0009.10.462
MA0014.10.38
MA0017.10.733
MA0018.20.603
MA0019.10.0312
MA0024.10.168
MA0025.10.912
MA0027.10.565
MA0028.10.281
MA0029.10.38
MA0030.12.03097e-4
MA0031.10.00398
MA0035.20.447
MA0038.10.532
MA0039.20.313
MA0040.10.78
MA0041.10.0265
MA0042.10.0977
MA0043.10.563
MA0046.10.186
MA0047.20.00164
MA0048.10.0217
MA0050.10.0431
MA0051.10.0173
MA0052.15.85386e-6
MA0055.10.189
MA0057.10.621
MA0058.10.551
MA0059.10.0315
MA0060.10.531
MA0061.10.0024
MA0062.20.0599
MA0065.20.0946
MA0066.10.0763
MA0067.10.0486
MA0068.19.12001e-4
MA0069.10.0922
MA0070.10.699
MA0071.10.567
MA0072.10.734
MA0073.10.893
MA0074.10.595
MA0076.10.464
MA0077.10.425
MA0078.10.0148
MA0079.20.0432
MA0080.20.00874
MA0081.10.291
MA0083.10.694
MA0084.10.548
MA0087.10.411
MA0088.10.06
MA0090.10.0072
MA0091.10.261
MA0092.10.634
MA0093.10.452
MA0099.26.17197e-13
MA0100.10.494
MA0101.10.0298
MA0102.20.513
MA0103.10.065
MA0104.20.00798
MA0105.11.99175e-9
MA0106.10.0498
MA0107.10.0335
MA0108.21.59222e-6
MA0111.10.901
MA0112.20.102
MA0113.10.0316
MA0114.10.279
MA0115.10.202
MA0116.14.98069e-5
MA0117.10.366
MA0119.10.473
MA0122.10.0944
MA0124.10.771
MA0125.10.489
MA0131.10.634
MA0135.10.119
MA0136.10.00707
MA0137.23.8898e-4
MA0138.20.943
MA0139.10.846
MA0140.10.189
MA0141.10.337
MA0142.10.259
MA0143.10.0587
MA0144.10.191
MA0145.10.182
MA0146.10.219
MA0147.10.00103
MA0148.10.00128
MA0149.10.081
MA0150.10.00165
MA0152.10.429
MA0153.10.0257
MA0154.10.037
MA0155.10.852
MA0156.10.0263
MA0157.10.0724
MA0159.10.611
MA0160.10.42
MA0162.10.46
MA0163.11.1513e-12
MA0164.10.141
MA0258.10.0288
MA0259.10.0557



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: CNhs10634

Novel motifP-value
10.111
100.00773
1000.21
1010.619
1020.486
1030.168
1040.318
1050.372
1060.231
1070.944
1080.773
1090.139
110.0308
1100.0744
1110.0184
1120.915
1130.543
1140.0185
1150.934
1160.526
1170.0425
1180.148
1190.14
120.539
1200.0351
1210.91
1220.26
1230.00971
1240.934
1250.28
1260.352
1270.572
1280.274
1290.514
130.232
1300.231
1310.408
1320.0998
1330.225
1340.46
1350.792
1360.708
1370.221
1380.433
1390.288
140.962
1400.62
1410.752
1420.601
1430.00644
1440.702
1450.496
1460.781
1470.805
1480.0092
1490.624
150.142
1500.439
1510.523
1520.164
1530.527
1540.196
1550.199
1560.113
1570.896
1580.258
1590.809
160.104
1600.68
1610.265
1620.931
1630.114
1640.256
1650.898
1660.502
1670.118
1680.83
1690.38
170.184
180.00671
190.929
20.509
200.282
210.497
220.971
230.619
240.697
250.621
260.013
270.832
280.79
290.0416
30.111
300.0328
310.712
320.0163
330.601
340.67
350.268
360.0071
370.239
380.753
390.322
40.259
400.167
410.134
420.219
430.117
440.681
450.376
460.0326
470.041
480.11
490.0324
50.528
500.645
510.566
520.664
530.482
540.557
550.682
560.746
570.124
580.685
590.948
60.482
600.763
610.184
620.268
630.663
640.191
650.504
660.106
670.816
680.606
690.722
70.688
700.0637
710.0199
720.92
730.508
740.278
750.0315
760.0531
770.535
780.248
790.249
80.0411
800.354
810.0502
820.369
830.41
840.428
850.461
860.498
870.408
880.798
890.856
90.857
900.0978
910.933
920.639
930.672
940.0741
950.227
960.395
970.454
980.628
990.563



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: CNhs10634


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)
0007023 (adult organism)
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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