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FF:11604-120I2: 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 17:11, 29 March 2012


Name:Hepatic Stellate Cells (lipocyte), donor2
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 typeadipocyte, lipocyte of liver
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC5305
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.0587
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-0.318
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12093

Jaspar motifP-value
MA0002.20.449
MA0003.10.157
MA0004.10.888
MA0006.10.33
MA0007.10.105
MA0009.10.191
MA0014.10.719
MA0017.10.0714
MA0018.20.00454
MA0019.10.556
MA0024.10.0029
MA0025.10.104
MA0027.10.735
MA0028.10.00304
MA0029.10.189
MA0030.10.134
MA0031.10.0915
MA0035.20.081
MA0038.10.998
MA0039.20.943
MA0040.10.285
MA0041.10.218
MA0042.10.523
MA0043.13.56181e-5
MA0046.10.326
MA0047.20.724
MA0048.10.961
MA0050.10.0015
MA0051.10.00182
MA0052.10.0845
MA0055.10.648
MA0057.10.38
MA0058.10.601
MA0059.10.717
MA0060.10.428
MA0061.10.619
MA0062.23.02934e-7
MA0065.20.0465
MA0066.10.0885
MA0067.10.0477
MA0068.10.902
MA0069.10.523
MA0070.10.00502
MA0071.10.0383
MA0072.10.488
MA0073.10.714
MA0074.10.144
MA0076.17.1542e-5
MA0077.10.35
MA0078.10.103
MA0079.20.753
MA0080.25.02702e-5
MA0081.10.04
MA0083.18.12252e-6
MA0084.10.47
MA0087.10.277
MA0088.10.675
MA0090.10.00325
MA0091.11.95292e-5
MA0092.10.186
MA0093.10.767
MA0099.20.767
MA0100.10.0961
MA0101.10.485
MA0102.20.00288
MA0103.10.623
MA0104.20.496
MA0105.10.329
MA0106.10.281
MA0107.10.628
MA0108.21.58833e-8
MA0111.10.547
MA0112.20.00113
MA0113.10.0317
MA0114.10.142
MA0115.10.773
MA0116.10.179
MA0117.10.418
MA0119.10.0578
MA0122.10.866
MA0124.10.266
MA0125.10.844
MA0131.10.137
MA0135.10.337
MA0136.15.83815e-10
MA0137.20.00913
MA0138.20.142
MA0139.10.846
MA0140.10.147
MA0141.10.0416
MA0142.10.677
MA0143.10.488
MA0144.10.895
MA0145.10.0783
MA0146.10.0468
MA0147.10.647
MA0148.10.809
MA0149.10.485
MA0150.10.531
MA0152.10.909
MA0153.10.0263
MA0154.10.0726
MA0155.10.0183
MA0156.19.94603e-8
MA0157.10.291
MA0159.10.363
MA0160.10.321
MA0162.10.116
MA0163.10.0534
MA0164.10.984
MA0258.10.00294
MA0259.10.348



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: CNhs12093

Novel motifP-value
10.651
100.588
1000.655
1010.827
1020.476
1030.417
1040.217
1050.202
1060.025
1070.0114
1080.456
1090.263
110.0778
1100.146
1110.96
1120.705
1130.428
1140.395
1150.106
1160.0838
1170.995
1180.722
1190.41
120.934
1200.402
1210.812
1220.974
1230.288
1240.311
1250.45
1260.615
1270.541
1280.0465
1290.199
130.581
1300.535
1310.511
1320.249
1330.815
1340.198
1350.183
1360.669
1370.144
1380.905
1390.0997
140.699
1400.674
1410.717
1420.588
1430.104
1440.8
1450.418
1460.413
1470.173
1480.981
1490.0034
150.805
1500.39
1510.343
1520.126
1530.646
1540.567
1550.694
1560.938
1570.217
1580.652
1590.478
160.108
1600.0185
1610.421
1620.0815
1630.952
1640.821
1650.242
1660.431
1670.043
1680.511
1690.0402
170.231
180.0926
190.0365
20.159
200.377
210.488
220.0856
230.123
240.991
250.659
260.0766
270.265
280.388
290.95
30.587
300.173
310.323
323.85586e-9
330.892
340.144
350.916
360.513
370.311
380.366
390.345
40.489
400.0943
410.683
420.837
430.218
440.298
450.211
460.135
470.426
480.286
490.216
50.658
500.393
510.272
520.208
530.989
540.31
550.36
560.291
570.388
580.948
590.0336
60.396
600.214
610.976
620.631
630.204
640.267
650.0385
660.915
670.467
680.0382
690.0681
70.656
700.0485
710.226
720.896
730.19
740.124
750.682
760.456
770.0371
780.771
790.00738
80.101
800.67
810.512
820.157
830.908
840.32
850.053
860.958
870.678
880.269
890.0826
90.127
900.429
910.302
920.224
930.473
940.412
950.566
960.769
970.315
980.62
990.011



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: CNhs12093


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)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000151 (secretory cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000327 (extracellular matrix secreting cell)
0000499 (stromal cell)
0000548 (animal cell)
0000632 (hepatic stellate cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic 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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