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FF:11601-120H8: 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 Sinusoidal Endothelial Cells, 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 typehepatic sinusoidal endothelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:sc05
catalog numberSC5005
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-0.157
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-0.157
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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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: CNhs12092

Jaspar motifP-value
MA0002.20.168
MA0003.10.186
MA0004.10.523
MA0006.10.329
MA0007.10.0582
MA0009.10.705
MA0014.10.627
MA0017.10.228
MA0018.20.0101
MA0019.10.317
MA0024.10.0371
MA0025.10.921
MA0027.10.419
MA0028.14.2207e-4
MA0029.10.259
MA0030.10.0964
MA0031.10.0381
MA0035.20.0183
MA0038.10.646
MA0039.20.992
MA0040.10.453
MA0041.10.36
MA0042.10.82
MA0043.18.13913e-4
MA0046.10.07
MA0047.20.411
MA0048.10.766
MA0050.11.05287e-4
MA0051.10.00358
MA0052.10.0463
MA0055.10.625
MA0057.10.212
MA0058.10.636
MA0059.10.272
MA0060.10.495
MA0061.10.171
MA0062.21.19908e-7
MA0065.20.0441
MA0066.10.0533
MA0067.10.0799
MA0068.10.868
MA0069.10.907
MA0070.10.00846
MA0071.10.021
MA0072.10.557
MA0073.10.747
MA0074.10.374
MA0076.14.76126e-6
MA0077.10.00391
MA0078.10.0274
MA0079.20.917
MA0080.20.658
MA0081.10.223
MA0083.11.18894e-4
MA0084.10.945
MA0087.10.516
MA0088.10.811
MA0090.10.0682
MA0091.10.0899
MA0092.10.276
MA0093.10.598
MA0099.22.598e-5
MA0100.10.246
MA0101.10.51
MA0102.27.6544e-5
MA0103.10.472
MA0104.20.848
MA0105.10.216
MA0106.10.158
MA0107.10.192
MA0108.22.46255e-12
MA0111.10.646
MA0112.20.00369
MA0113.10.102
MA0114.10.483
MA0115.10.622
MA0116.10.144
MA0117.10.365
MA0119.10.0675
MA0122.10.831
MA0124.10.501
MA0125.10.773
MA0131.10.0715
MA0135.10.0722
MA0136.10.0419
MA0137.20.0578
MA0138.20.182
MA0139.10.986
MA0140.10.0574
MA0141.10.033
MA0142.10.476
MA0143.10.664
MA0144.10.724
MA0145.10.189
MA0146.10.102
MA0147.10.879
MA0148.10.239
MA0149.10.284
MA0150.10.178
MA0152.10.549
MA0153.10.372
MA0154.10.053
MA0155.10.041
MA0156.10.0306
MA0157.10.395
MA0159.10.316
MA0160.10.184
MA0162.10.0992
MA0163.10.149
MA0164.10.461
MA0258.10.00858
MA0259.10.779



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: CNhs12092

Novel motifP-value
10.655
100.521
1000.979
1010.651
1020.943
1030.621
1040.22
1050.0503
1060.0175
1070.00964
1080.286
1090.184
110.0785
1100.149
1110.8
1120.402
1130.951
1140.327
1150.763
1160.21
1170.941
1180.871
1190.228
120.636
1200.0995
1210.819
1220.611
1230.396
1240.864
1250.382
1260.799
1270.379
1280.0249
1290.196
130.431
1300.246
1310.56
1320.235
1330.289
1340.881
1350.138
1360.411
1370.538
1380.978
1390.087
140.865
1400.979
1410.879
1420.345
1430.00113
1440.856
1450.0855
1460.226
1470.251
1480.79
1490.0232
150.596
1500.189
1510.339
1520.0501
1530.382
1540.477
1550.844
1560.573
1570.146
1580.724
1590.822
160.241
1600.00862
1610.28
1620.206
1630.757
1640.89
1650.126
1660.921
1670.184
1680.341
1690.0283
170.123
180.0888
190.0759
20.214
200.363
210.714
220.113
230.0607
240.344
250.646
260.0628
270.206
280.364
290.893
30.488
300.31
310.388
329.41698e-4
330.542
340.147
350.659
360.607
370.291
380.236
390.302
40.252
400.0204
410.301
420.605
430.199
440.408
450.212
460.127
470.411
480.202
490.244
50.663
500.459
510.266
520.353
530.937
540.302
550.631
560.247
570.231
580.991
590.00797
60.752
600.239
610.811
620.73
630.21
640.201
650.0199
660.408
670.54
680.00372
690.0115
70.778
700.138
710.228
720.737
730.0595
740.877
750.914
760.265
770.0431
780.517
790.0209
80.0674
800.4
810.816
820.457
830.692
840.133
850.0528
860.84
870.433
880.548
890.109
90.139
900.0173
910.0826
920.262
930.6
940.462
950.228
960.997
970.434
980.4
990.0972



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: CNhs12092


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)
0000066 (epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002262 (endothelial cell of sinusoid)
0002321 (embryonic cell)
0002371 (somatic cell)
1000398 (endothelial cell of hepatic sinusoid)

UBERON: Anatomy
0000015 (anatomical boundary)
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000353 (parenchyma)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001009 (circulatory system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001280 (liver parenchyma)
0001281 (hepatic sinusoid)
0001555 (digestive tract)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003497 (abdomen blood vessel)
0003513 (trunk blood vessel)
0003835 (abdominal segment blood vessel)
0003894 (liver primordium)
0003909 (sinusoid)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004647 (liver lobule)
0004872 (splanchnic layer of lateral plate mesoderm)
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)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0006965 (vascular cord)
0007026 (primitive gut)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
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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