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FF:10043-101F7: 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 16:29, 29 March 2012


Name:thymus, fetal, 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 stage22-34 weeks fetus
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number5040223
catalog numberCat:636586
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-Basophils0.0262
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.145
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.00647
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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-Whole0.0262
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-Whole0.0508
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: CNhs10650

Jaspar motifP-value
MA0002.20.446
MA0003.10.598
MA0004.10.665
MA0006.10.903
MA0007.10.684
MA0009.10.849
MA0014.10.974
MA0017.10.0864
MA0018.20.0222
MA0019.10.28
MA0024.10.00401
MA0025.10.0408
MA0027.10.841
MA0028.10.0197
MA0029.10.676
MA0030.10.0158
MA0031.10.00161
MA0035.20.0707
MA0038.10.0201
MA0039.20.0219
MA0040.10.948
MA0041.10.892
MA0042.10.863
MA0043.10.393
MA0046.10.69
MA0047.20.206
MA0048.10.0146
MA0050.12.50626e-5
MA0051.10.0925
MA0052.10.227
MA0055.10.0322
MA0057.10.256
MA0058.10.888
MA0059.10.0166
MA0060.17.5864e-17
MA0061.10.587
MA0062.26.47524e-8
MA0065.20.00429
MA0066.10.0393
MA0067.10.856
MA0068.10.00437
MA0069.10.795
MA0070.10.131
MA0071.10.175
MA0072.10.561
MA0073.10.833
MA0074.10.0295
MA0076.11.19081e-4
MA0077.10.831
MA0078.10.18
MA0079.20.0327
MA0080.27.76745e-10
MA0081.10.00712
MA0083.10.916
MA0084.10.85
MA0087.10.72
MA0088.10.4
MA0090.10.0121
MA0091.10.702
MA0092.10.301
MA0093.10.751
MA0099.21.39536e-11
MA0100.10.0258
MA0101.10.928
MA0102.20.843
MA0103.10.192
MA0104.20.43
MA0105.10.0259
MA0106.10.0412
MA0107.10.674
MA0108.21.48202e-15
MA0111.10.837
MA0112.26.33888e-6
MA0113.10.834
MA0114.10.0124
MA0115.10.274
MA0116.10.0971
MA0117.10.89
MA0119.10.0185
MA0122.10.573
MA0124.10.325
MA0125.10.371
MA0131.10.135
MA0135.10.466
MA0136.16.92296e-12
MA0137.20.036
MA0138.20.311
MA0139.10.636
MA0140.10.255
MA0141.18.22725e-5
MA0142.10.0801
MA0143.10.0229
MA0144.10.792
MA0145.10.131
MA0146.10.215
MA0147.10.245
MA0148.10.856
MA0149.10.0264
MA0150.17.91797e-4
MA0152.10.211
MA0153.10.885
MA0154.10.191
MA0155.10.953
MA0156.15.12628e-11
MA0157.10.0562
MA0159.10.0307
MA0160.10.0334
MA0162.10.0923
MA0163.13.20058e-4
MA0164.10.47
MA0258.10.00244
MA0259.10.712



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: CNhs10650

Novel motifP-value
10.0341
100.104
1000.346
1010.8
1020.991
1030.263
1040.864
1050.444
1060.00905
1070.055
1080.213
1090.0816
110.143
1100.0992
1110.0277
1120.139
1130.149
1144.04424e-4
1150.131
1160.137
1170.681
1180.116
1190.115
120.739
1200.348
1210.133
1220.616
1230.699
1240.318
1250.406
1260.571
1270.806
1280.0652
1290.819
130.248
1300.0247
1310.745
1320.768
1330.592
1340.764
1350.0915
1360.739
1370.307
1380.585
1390.0822
140.664
1400.0178
1410.129
1420.088
1430.784
1440.429
1450.431
1460.562
1470.242
1480.079
1490.0713
150.16
1500.359
1510.538
1520.0355
1530.978
1540.438
1550.415
1560.304
1570.324
1580.966
1590.882
160.0759
1600.0982
1610.74
1620.365
1630.636
1640.0182
1650.972
1660.655
1670.0788
1680.454
1690.00121
170.152
180.0468
190.025
20.786
200.236
210.608
220.152
230.293
240.856
250.694
260.122
270.542
280.741
290.291
30.221
300.505
310.339
320.00731
330.38
340.974
350.246
360.103
370.0382
380.508
390.285
40.938
400.281
410.435
420.87
430.229
440.483
450.847
460.0755
470.296
480.475
490.289
50.314
500.959
510.452
520.51
530.646
540.426
550.234
560.721
570.0544
580.888
590.182
60.626
600.352
610.854
620.553
630.288
640.245
650.261
660.198
670.166
680.448
690.508
70.862
700.0119
710.0636
720.49
730.015
740.574
750.231
760.19
770.0416
780.663
790.289
80.00402
800.0055
810.304
820.247
830.865
840.337
850.0184
860.914
870.375
880.323
890.00868
90.933
900.0485
910.563
920.158
930.82
940.246
950.184
960.813
970.624
980.0718
990.141



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: CNhs10650


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)
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