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FF:10062-101H8: 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:stomach, 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
tissuestomach
dev stage40 weeks fetus
sexfemale
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 numberA805052
catalog numberCat:RtHFN: Stomach
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-penis0.0144
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-0.0991
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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: CNhs11771

Jaspar motifP-value
MA0002.29.99126e-4
MA0003.10.767
MA0004.10.214
MA0006.10.277
MA0007.10.733
MA0009.10.703
MA0014.10.441
MA0017.10.606
MA0018.20.172
MA0019.10.764
MA0024.10.536
MA0025.10.504
MA0027.10.948
MA0028.14.10197e-4
MA0029.10.301
MA0030.10.00528
MA0031.10.0331
MA0035.20.0469
MA0038.10.901
MA0039.20.937
MA0040.10.745
MA0041.10.995
MA0042.10.893
MA0043.10.472
MA0046.11.66668e-17
MA0047.25.08202e-7
MA0048.10.233
MA0050.10.338
MA0051.10.217
MA0052.10.00762
MA0055.10.0377
MA0057.10.793
MA0058.10.0584
MA0059.10.00594
MA0060.10.943
MA0061.10.00294
MA0062.27.74459e-6
MA0065.20.0354
MA0066.10.00244
MA0067.10.098
MA0068.10.0401
MA0069.10.531
MA0070.10.512
MA0071.10.326
MA0072.10.226
MA0073.10.447
MA0074.10.596
MA0076.11.91476e-5
MA0077.10.535
MA0078.10.64
MA0079.20.329
MA0080.20.0137
MA0081.10.00391
MA0083.16.51111e-7
MA0084.10.573
MA0087.10.211
MA0088.10.00948
MA0090.10.155
MA0091.10.337
MA0092.10.663
MA0093.10.181
MA0099.21.78894e-9
MA0100.10.0985
MA0101.10.0168
MA0102.20.625
MA0103.10.363
MA0104.20.00298
MA0105.19.60675e-8
MA0106.10.00323
MA0107.10.0236
MA0108.25.93165e-16
MA0111.10.851
MA0112.20.0111
MA0113.10.118
MA0114.10.177
MA0115.10.106
MA0116.18.7531e-5
MA0117.10.499
MA0119.10.683
MA0122.10.69
MA0124.10.742
MA0125.10.798
MA0131.10.805
MA0135.10.234
MA0136.14.94018e-4
MA0137.20.979
MA0138.20.745
MA0139.10.00878
MA0140.10.802
MA0141.10.0632
MA0142.10.0351
MA0143.10.19
MA0144.10.675
MA0145.10.835
MA0146.10.199
MA0147.10.00244
MA0148.15.14874e-4
MA0149.10.231
MA0150.14.15711e-4
MA0152.10.211
MA0153.15.39602e-9
MA0154.10.0018
MA0155.10.76
MA0156.12.46114e-4
MA0157.10.81
MA0159.10.0488
MA0160.10.203
MA0162.10.405
MA0163.12.91172e-9
MA0164.10.103
MA0258.10.171
MA0259.10.129



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: CNhs11771

Novel motifP-value
10.0114
100.0421
1000.221
1010.614
1020.505
1030.0306
1040.901
1050.686
1060.875
1070.193
1080.607
1090.0316
110.0682
1100.0429
1110.0855
1120.345
1130.00194
1140.00138
1150.719
1160.745
1170.00542
1180.025
1190.642
120.581
1200.00987
1210.795
1220.834
1230.324
1240.357
1250.126
1260.66
1270.0263
1280.253
1290.246
130.0727
1300.892
1310.98
1320.0678
1330.0643
1340.454
1350.926
1360.885
1370.213
1380.974
1390.298
140.655
1400.686
1410.968
1420.515
1430.0046
1440.7
1450.7
1460.73
1470.987
1480.231
1490.231
150.0909
1500.515
1510.852
1520.65
1530.878
1540.704
1550.369
1560.917
1570.555
1580.443
1590.367
160.171
1600.209
1610.385
1620.912
1630.925
1640.0223
1650.508
1660.44
1670.124
1680.367
1690.132
170.943
180.00446
190.91
20.38
200.258
210.0757
220.527
230.601
240.0496
250.335
260.494
270.53
280.807
290.00666
30.0837
300.133
310.908
320.0704
330.113
340.364
350.0781
360.0172
370.046
380.691
390.835
40.586
400.163
410.0251
420.184
430.195
440.174
450.662
460.071
470.0349
480.117
490.296
50.326
500.485
510.817
520.17
530.646
540.765
550.377
560.548
570.28
580.397
590.298
60.321
600.784
610.836
620.202
630.657
640.368
650.968
660.175
670.0914
680.587
690.695
70.463
700.0411
710.0173
720.417
730.326
740.15
750.0089
760.0975
770.769
780.845
790.149
80.167
800.47
810.169
820.0823
830.717
840.731
850.824
860.32
870.0673
880.791
890.0535
90.797
900.0227
910.879
920.945
930.0267
940.00883
950.0382
960.885
970.314
980.2
990.427



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: CNhs11771


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)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
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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