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FF:11218-116B3: 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 16:34, 29 March 2012


Name:Mesenchymal stem cells - hepatic, donor0
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number7525
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-penis-0.0729
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-0.128
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs10845

Jaspar motifP-value
MA0002.20.0822
MA0003.10.386
MA0004.10.0271
MA0006.10.522
MA0007.10.0377
MA0009.10.885
MA0014.10.62
MA0017.10.609
MA0018.20.0195
MA0019.10.451
MA0024.16.55769e-4
MA0025.10.0546
MA0027.10.447
MA0028.10.0466
MA0029.10.594
MA0030.10.867
MA0031.10.384
MA0035.20.985
MA0038.10.631
MA0039.20.112
MA0040.10.0185
MA0041.10.399
MA0042.10.428
MA0043.10.536
MA0046.10.998
MA0047.20.784
MA0048.10.169
MA0050.10.00704
MA0051.10.013
MA0052.10.866
MA0055.10.65
MA0057.10.958
MA0058.10.0112
MA0059.10.327
MA0060.10.13
MA0061.10.579
MA0062.24.76448e-9
MA0065.20.541
MA0066.10.319
MA0067.10.124
MA0068.10.586
MA0069.10.512
MA0070.10.687
MA0071.10.1
MA0072.10.699
MA0073.10.25
MA0074.10.46
MA0076.13.6331e-4
MA0077.10.0787
MA0078.10.997
MA0079.20.343
MA0080.21.99492e-9
MA0081.17.25576e-4
MA0083.14.91094e-6
MA0084.10.383
MA0087.10.159
MA0088.10.443
MA0090.17.88476e-6
MA0091.10.00233
MA0092.10.00578
MA0093.10.0333
MA0099.20.00239
MA0100.10.907
MA0101.10.0761
MA0102.20.628
MA0103.10.00275
MA0104.20.0881
MA0105.10.733
MA0106.10.691
MA0107.10.116
MA0108.23.62628e-5
MA0111.10.731
MA0112.20.011
MA0113.10.00442
MA0114.10.676
MA0115.10.0846
MA0116.10.176
MA0117.10.978
MA0119.13.50897e-4
MA0122.10.714
MA0124.10.807
MA0125.10.901
MA0131.10.71
MA0135.10.00872
MA0136.11.93579e-9
MA0137.20.85
MA0138.20.565
MA0139.10.877
MA0140.10.445
MA0141.10.765
MA0142.10.0238
MA0143.10.45
MA0144.10.623
MA0145.10.0753
MA0146.10.0951
MA0147.10.117
MA0148.10.195
MA0149.10.735
MA0150.10.919
MA0152.10.0473
MA0153.10.395
MA0154.10.121
MA0155.10.109
MA0156.11.5143e-9
MA0157.10.516
MA0159.10.165
MA0160.10.892
MA0162.10.177
MA0163.10.0355
MA0164.10.747
MA0258.10.161
MA0259.10.926



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: CNhs10845

Novel motifP-value
10.614
100.703
1000.175
1010.743
1020.13
1030.125
1040.372
1050.75
1060.309
1070.0933
1080.529
1090.644
110.524
1100.723
1110.514
1120.63
1130.582
1140.394
1150.296
1160.236
1170.8
1180.57
1190.604
120.464
1200.61
1210.264
1220.0546
1230.0322
1240.753
1250.103
1260.857
1270.907
1280.0711
1290.351
130.903
1300.00992
1310.121
1320.417
1330.73
1340.391
1350.625
1360.903
1370.272
1380.155
1390.127
140.512
1400.136
1410.495
1420.368
1430.692
1440.336
1450.719
1460.235
1470.431
1480.555
1490.00529
150.873
1500.561
1510.72
1520.0836
1530.8
1540.655
1550.25
1560.515
1570.121
1580.682
1590.899
160.0393
1600.0738
1610.792
1620.064
1630.069
1640.118
1650.79
1660.137
1670.278
1680.54
1690.0388
170.422
180.246
190.0327
20.246
200.859
210.299
220.0294
230.136
240.976
250.148
260.212
270.992
280.0754
290.274
30.45
300.705
310.148
321.68287e-17
330.889
340.537
350.368
360.521
370.262
380.997
390.125
40.485
400.588
410.0804
420.901
430.28
440.946
450.505
460.397
470.858
480.978
490.168
50.299
500.197
510.252
520.868
530.309
540.555
550.988
560.786
570.523
580.963
590.232
60.686
600.956
610.585
620.839
630.161
640.935
650.141
660.988
670.223
680.474
690.297
70.778
700.906
710.122
720.78
730.137
740.636
750.667
760.954
770.0107
780.502
790.275
80.11
800.61
810.831
820.93
830.0677
840.353
850.008
860.74
870.642
880.218
890.131
90.391
900.51
910.902
920.216
930.153
940.985
950.447
960.447
970.386
980.463
990.00828



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: CNhs10845


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)
0000548 (animal cell)
0000723 (somatic stem cell)
0002195 (hepatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002571 (hepatic mesenchymal stem cell)

UBERON: Anatomy
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002384 (connective tissue)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
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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