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FF:11249-116E7: 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 16:36, 29 March 2012


Name:Pancreatic stromal cells, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepancreas
dev stage39 years old adult
sexmale
age39
cell typepancreatic stromal cell
cell lineNA
companyCell systems
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.049
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-lymphoma0.252
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10877

Jaspar motifP-value
MA0002.20.0444
MA0003.10.67
MA0004.10.403
MA0006.10.306
MA0007.10.674
MA0009.10.756
MA0014.10.91
MA0017.10.296
MA0018.25.25978e-7
MA0019.10.798
MA0024.10.31
MA0025.10.00116
MA0027.10.592
MA0028.10.732
MA0029.10.804
MA0030.10.0798
MA0031.10.182
MA0035.20.0091
MA0038.10.701
MA0039.20.27
MA0040.10.757
MA0041.10.737
MA0042.10.877
MA0043.15.25152e-6
MA0046.10.976
MA0047.20.245
MA0048.10.0107
MA0050.10.883
MA0051.10.436
MA0052.10.122
MA0055.10.287
MA0057.10.3
MA0058.10.385
MA0059.10.137
MA0060.10.0287
MA0061.10.0213
MA0062.27.06142e-5
MA0065.20.116
MA0066.10.411
MA0067.10.00201
MA0068.10.895
MA0069.10.121
MA0070.10.98
MA0071.10.385
MA0072.10.254
MA0073.10.845
MA0074.10.594
MA0076.10.663
MA0077.10.159
MA0078.10.153
MA0079.20.611
MA0080.25.52576e-10
MA0081.10.0331
MA0083.10.867
MA0084.10.0134
MA0087.10.8
MA0088.10.0296
MA0090.10.0129
MA0091.10.0484
MA0092.10.534
MA0093.10.44
MA0099.20.007
MA0100.10.598
MA0101.10.0145
MA0102.20.462
MA0103.19.37311e-5
MA0104.20.0181
MA0105.10.85
MA0106.10.0179
MA0107.18.79082e-4
MA0108.20.732
MA0111.10.206
MA0112.20.439
MA0113.10.97
MA0114.10.142
MA0115.10.499
MA0116.10.93
MA0117.10.0979
MA0119.10.65
MA0122.10.271
MA0124.10.672
MA0125.10.418
MA0131.10.897
MA0135.10.379
MA0136.18.67073e-11
MA0137.20.756
MA0138.20.78
MA0139.10.698
MA0140.10.0117
MA0141.10.308
MA0142.10.0359
MA0143.10.983
MA0144.10.693
MA0145.10.684
MA0146.10.836
MA0147.10.0262
MA0148.10.0974
MA0149.10.94
MA0150.10.00172
MA0152.10.0213
MA0153.10.217
MA0154.10.599
MA0155.10.949
MA0156.17.8661e-8
MA0157.10.201
MA0159.10.337
MA0160.10.0572
MA0162.10.0121
MA0163.10.0484
MA0164.10.915
MA0258.10.312
MA0259.10.382



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: CNhs10877

Novel motifP-value
10.227
100.515
1000.379
1010.666
1020.155
1030.949
1040.766
1050.416
1060.101
1070.803
1080.324
1090.824
110.693
1100.431
1110.131
1120.924
1131.12255e-4
1140.514
1150.213
1160.23
1170.361
1180.917
1190.105
120.369
1200.328
1210.343
1220.00808
1230.00121
1240.798
1250.606
1260.685
1270.673
1280.838
1290.445
130.544
1300.115
1310.206
1320.21
1330.183
1340.433
1350.28
1360.997
1370.0948
1380.0927
1392.8164e-5
140.181
1400.282
1410.0653
1420.662
1430.486
1440.375
1450.921
1460.726
1470.22
1480.284
1490.386
150.0781
1500.269
1510.384
1520.388
1530.874
1540.753
1556.08828e-4
1560.939
1570.0577
1586.80512e-4
1590.179
160.353
1600.696
1610.602
1620.754
1630.529
1640.888
1650.628
1660.088
1670.342
1680.848
1690.174
170.615
180.972
190.00308
20.641
200.588
210.0105
220.6
230.376
240.961
250.25
260.707
270.963
280.27
290.679
30.735
300.348
310.898
321.03259e-4
330.757
340.897
350.194
360.0285
370.0789
380.21
390.381
40.0176
400.0304
410.325
420.251
430.347
440.984
450.982
460.622
470.758
480.671
490.0471
50.24
500.342
510.846
520.784
530.262
540.624
550.19
560.913
570.73
580.13
590.722
60.696
600.0886
610.509
620.202
630.868
640.513
650.527
660.862
670.853
680.666
690.448
70.0319
700.0449
710.503
720.684
730.34
740.082
750.77
760.846
770.331
780.071
790.048
80.933
800.104
810.524
820.575
830.125
840.994
850.359
860.288
870.137
880.335
890.781
90.582
900.113
910.772
920.711
930.385
940.436
950.202
960.298
970.545
980.122
990.00261



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: CNhs10877


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000499 (stromal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002574 (stromal cell of pancreas)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
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)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002384 (connective tissue)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
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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