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FF:10029-101E2: 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:trachea, 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
tissuetrachea
dev stage59,72,78 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 -20
catalog numberCat:AM6000 Lot:0910061 -20
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-0.0947
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.00354
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.214
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.0301
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.0301
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-Whole0.0301
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: CNhs10635

Jaspar motifP-value
MA0002.20.917
MA0003.10.177
MA0004.10.0843
MA0006.10.0775
MA0007.10.849
MA0009.10.625
MA0014.10.811
MA0017.10.174
MA0018.20.212
MA0019.10.0205
MA0024.10.0885
MA0025.10.453
MA0027.10.718
MA0028.10.00388
MA0029.10.15
MA0030.12.70801e-6
MA0031.10.00407
MA0035.20.711
MA0038.10.904
MA0039.20.0322
MA0040.10.605
MA0041.10.0765
MA0042.10.174
MA0043.10.711
MA0046.10.0451
MA0047.26.62716e-8
MA0048.10.0107
MA0050.10.0452
MA0051.10.044
MA0052.13.49425e-4
MA0055.10.00645
MA0057.10.678
MA0058.10.0382
MA0059.10.0174
MA0060.10.141
MA0061.10.0525
MA0062.20.00371
MA0065.20.499
MA0066.10.284
MA0067.10.12
MA0068.10.076
MA0069.10.373
MA0070.10.889
MA0071.10.0264
MA0072.10.048
MA0073.10.985
MA0074.10.665
MA0076.10.00584
MA0077.10.221
MA0078.10.377
MA0079.20.0719
MA0080.20.00112
MA0081.10.888
MA0083.10.00903
MA0084.10.696
MA0087.10.0741
MA0088.10.0168
MA0090.10.205
MA0091.10.541
MA0092.10.884
MA0093.10.102
MA0099.28.01012e-4
MA0100.10.749
MA0101.10.248
MA0102.20.0956
MA0103.10.00684
MA0104.20.0059
MA0105.16.66095e-4
MA0106.10.567
MA0107.10.322
MA0108.25.73181e-33
MA0111.10.603
MA0112.20.779
MA0113.10.175
MA0114.10.74
MA0115.10.833
MA0116.10.018
MA0117.10.21
MA0119.10.721
MA0122.10.148
MA0124.10.484
MA0125.10.759
MA0131.10.233
MA0135.10.157
MA0136.16.27306e-4
MA0137.21.25788e-6
MA0138.20.191
MA0139.10.599
MA0140.10.158
MA0141.10.164
MA0142.10.723
MA0143.10.836
MA0144.12.96159e-5
MA0145.10.0138
MA0146.10.928
MA0147.10.00309
MA0148.12.09833e-7
MA0149.10.0585
MA0150.10.0187
MA0152.10.948
MA0153.10.00117
MA0154.10.892
MA0155.10.603
MA0156.10.0707
MA0157.10.0892
MA0159.10.854
MA0160.10.228
MA0162.10.709
MA0163.14.84548e-5
MA0164.10.293
MA0258.10.431
MA0259.10.0484



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: CNhs10635

Novel motifP-value
10.156
100.00786
1000.199
1010.91
1020.89
1030.687
1040.74
1050.476
1060.541
1070.12
1080.985
1090.756
110.342
1100.364
1110.0647
1120.399
1130.621
1140.139
1150.568
1160.205
1170.0869
1180.0892
1190.374
120.908
1200.328
1210.35
1220.421
1230.00333
1240.479
1250.454
1260.126
1270.674
1280.446
1290.347
130.3
1300.611
1310.513
1320.164
1330.00898
1340.0074
1350.0408
1360.813
1370.787
1380.622
1390.47
140.847
1400.207
1410.449
1420.994
1430.114
1440.145
1450.63
1460.0955
1470.452
1480.496
1490.748
150.228
1500.945
1510.668
1520.037
1530.509
1540.485
1550.739
1560.513
1570.619
1580.15
1590.731
160.792
1600.43
1610.195
1620.964
1630.602
1640.0451
1650.27
1660.922
1670.023
1680.0284
1690.339
170.903
180.049
190.698
20.0195
200.147
210.234
220.402
230.302
240.568
250.777
260.325
270.557
280.959
290.0692
30.394
300.00597
310.968
320.975
330.813
340.406
350.133
360.0283
370.504
380.944
390.322
40.287
400.324
410.253
420.579
430.366
440.941
450.0503
460.326
470.259
480.498
490.0652
50.722
500.273
510.528
520.103
530.942
540.986
550.874
560.929
570.101
580.868
590.279
60.328
600.344
610.674
620.631
630.621
640.511
650.896
660.0505
670.393
680.672
690.827
70.976
700.281
710.0681
720.484
730.732
740.324
750.0209
760.0103
770.012
780.0132
790.141
80.687
800.0221
810.217
820.723
830.345
840.839
850.702
860.959
870.618
880.977
890.365
90.233
900.0241
910.439
920.685
930.144
940.0309
950.508
960.636
970.835
980.149
990.31



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: CNhs10635


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)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001005 (respiratory airway)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001558 (lower respiratory tract)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003126 (trachea)
0003127 (open tracheal system trachea)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)
0007196 (tracheobronchial tree)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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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