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FF:10058-101H4: 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:trachea, 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
tissuetrachea
dev stage29 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 numberB402231
catalog numberCat:RtHFN: Trachea
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-penis0.084
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-0.129
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11766

Jaspar motifP-value
MA0002.21.24365e-5
MA0003.10.84
MA0004.10.012
MA0006.10.438
MA0007.10.307
MA0009.10.381
MA0014.10.232
MA0017.10.136
MA0018.20.354
MA0019.10.847
MA0024.10.246
MA0025.10.506
MA0027.10.846
MA0028.14.63707e-6
MA0029.10.294
MA0030.10.353
MA0031.10.982
MA0035.20.134
MA0038.10.385
MA0039.20.348
MA0040.10.507
MA0041.10.646
MA0042.10.931
MA0043.10.00987
MA0046.10.0676
MA0047.20.31
MA0048.10.269
MA0050.10.044
MA0051.10.0738
MA0052.13.16532e-8
MA0055.10.00265
MA0057.10.787
MA0058.10.00546
MA0059.10.00614
MA0060.10.00407
MA0061.11.62161e-5
MA0062.21.93481e-11
MA0065.20.00636
MA0066.10.0158
MA0067.10.0203
MA0068.10.00308
MA0069.10.775
MA0070.10.704
MA0071.10.24
MA0072.10.0662
MA0073.10.4
MA0074.10.71
MA0076.14.93133e-7
MA0077.10.836
MA0078.10.426
MA0079.20.92
MA0080.25.7276e-7
MA0081.10.00699
MA0083.10.417
MA0084.10.0676
MA0087.10.158
MA0088.10.00843
MA0090.10.138
MA0091.10.576
MA0092.10.458
MA0093.10.013
MA0099.22.14805e-21
MA0100.10.0935
MA0101.12.23669e-5
MA0102.20.174
MA0103.10.647
MA0104.27.66828e-4
MA0105.11.47502e-8
MA0106.10.051
MA0107.12.87975e-5
MA0108.23.28186e-18
MA0111.10.666
MA0112.20.225
MA0113.10.404
MA0114.10.0157
MA0115.10.666
MA0116.13.17815e-4
MA0117.10.21
MA0119.10.812
MA0122.10.57
MA0124.10.659
MA0125.10.606
MA0131.10.753
MA0135.10.216
MA0136.19.76623e-11
MA0137.20.767
MA0138.20.475
MA0139.10.00889
MA0140.10.0834
MA0141.10.0812
MA0142.10.0274
MA0143.10.573
MA0144.10.997
MA0145.10.415
MA0146.10.125
MA0147.14.27345e-4
MA0148.10.217
MA0149.10.0136
MA0150.11.64368e-10
MA0152.10.0136
MA0153.10.549
MA0154.10.0133
MA0155.10.488
MA0156.11.22291e-10
MA0157.10.594
MA0159.10.182
MA0160.10.0241
MA0162.10.904
MA0163.12.98634e-6
MA0164.10.485
MA0258.10.326
MA0259.10.0786



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: CNhs11766

Novel motifP-value
10.0463
100.0424
1000.683
1010.728
1020.41
1030.102
1040.623
1050.819
1060.977
1070.133
1080.47
1090.00491
110.0924
1100.127
1110.0751
1120.987
1135.06755e-4
1140.011
1150.162
1160.652
1170.00824
1180.0332
1190.378
120.421
1200.435
1210.729
1220.0994
1230.522
1240.161
1250.38
1260.532
1270.198
1280.612
1290.289
130.185
1300.948
1310.601
1320.0305
1330.0985
1340.606
1350.655
1360.178
1370.344
1380.363
1390.295
140.722
1400.753
1410.521
1420.701
1430.00304
1440.965
1450.944
1460.715
1470.0937
1480.302
1490.773
150.0233
1500.409
1510.97
1520.744
1530.464
1540.652
1550.252
1560.993
1570.658
1580.112
1590.939
160.934
1600.725
1610.201
1620.387
1630.195
1640.137
1650.304
1660.0823
1670.0184
1680.818
1690.149
170.431
180.0254
190.504
20.133
200.11
210.588
220.482
230.812
240.175
250.464
260.0515
270.655
280.569
290.0204
30.188
300.08
310.94
321.75312e-4
330.194
340.644
350.147
360.03
370.0915
380.576
390.455
40.385
400.048
410.0635
420.202
430.0972
440.763
450.649
460.15
470.0636
480.201
490.0722
50.372
500.586
510.44
520.23
530.964
540.74
550.226
560.729
570.447
580.304
590.632
60.987
600.766
610.125
620.228
630.954
640.248
650.871
660.0116
670.368
680.526
690.538
70.452
700.122
710.0524
720.249
730.176
740.249
750.00862
760.159
770.613
780.169
790.623
80.2
800.37
810.409
820.603
830.828
840.841
850.772
860.315
870.0177
880.596
890.983
90.956
900.0555
910.301
920.967
930.331
940.0491
950.0047
960.248
970.939
980.337
990.199



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: CNhs11766


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)
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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