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FF:11524-119I3: 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 16:45, 29 March 2012


Name:Hepatic Stellate Cells (lipocyte), donor1
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-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-0.117
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-0.21
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: CNhs11335

Jaspar motifP-value
MA0002.20.988
MA0003.10.239
MA0004.10.746
MA0006.10.238
MA0007.10.0599
MA0009.10.263
MA0014.10.897
MA0017.10.098
MA0018.26.54865e-4
MA0019.10.611
MA0024.10.00368
MA0025.10.0864
MA0027.10.302
MA0028.10.00407
MA0029.10.0778
MA0030.10.393
MA0031.10.344
MA0035.20.035
MA0038.10.0561
MA0039.20.485
MA0040.10.599
MA0041.10.306
MA0042.10.798
MA0043.17.15612e-5
MA0046.14.68085e-6
MA0047.20.567
MA0048.10.604
MA0050.11.03412e-5
MA0051.10.00383
MA0052.10.396
MA0055.10.147
MA0057.10.331
MA0058.10.428
MA0059.10.859
MA0060.10.265
MA0061.10.75
MA0062.21.90516e-7
MA0065.20.423
MA0066.10.45
MA0067.10.00101
MA0068.10.852
MA0069.10.977
MA0070.10.0252
MA0071.10.097
MA0072.10.945
MA0073.10.873
MA0074.10.317
MA0076.15.47735e-5
MA0077.10.575
MA0078.10.584
MA0079.20.537
MA0080.21.00055e-5
MA0081.10.0227
MA0083.12.08279e-4
MA0084.10.778
MA0087.10.26
MA0088.10.951
MA0090.11.78923e-4
MA0091.10.00561
MA0092.10.0379
MA0093.10.694
MA0099.20.874
MA0100.10.272
MA0101.10.447
MA0102.20.00104
MA0103.10.749
MA0104.20.276
MA0105.10.878
MA0106.10.235
MA0107.10.573
MA0108.29.77038e-7
MA0111.10.286
MA0112.20.0117
MA0113.10.0171
MA0114.10.157
MA0115.10.872
MA0116.10.498
MA0117.10.226
MA0119.10.108
MA0122.10.853
MA0124.10.365
MA0125.10.633
MA0131.10.111
MA0135.10.47
MA0136.15.27802e-10
MA0137.20.909
MA0138.20.26
MA0139.10.786
MA0140.10.134
MA0141.10.115
MA0142.10.517
MA0143.10.705
MA0144.10.257
MA0145.10.0928
MA0146.10.0503
MA0147.10.376
MA0148.10.517
MA0149.10.447
MA0150.10.149
MA0152.10.601
MA0153.12.93136e-5
MA0154.10.253
MA0155.10.021
MA0156.17.90517e-7
MA0157.10.316
MA0159.10.593
MA0160.10.251
MA0162.10.149
MA0163.10.536
MA0164.10.644
MA0258.10.0455
MA0259.10.313



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: CNhs11335

Novel motifP-value
10.781
100.0937
1000.652
1010.587
1020.588
1030.66
1040.369
1050.0559
1060.0823
1070.00971
1080.848
1090.481
110.258
1100.183
1110.231
1120.615
1130.364
1140.589
1150.534
1160.0265
1170.335
1180.942
1190.715
120.583
1200.969
1210.878
1220.354
1230.00938
1240.659
1250.205
1260.83
1270.959
1280.0855
1290.897
130.869
1300.214
1310.588
1320.22
1330.348
1340.244
1350.223
1360.53
1370.141
1380.367
1390.832
140.953
1400.989
1410.575
1420.875
1430.186
1440.726
1450.439
1460.238
1470.621
1480.447
1490.00998
150.788
1500.321
1510.502
1520.104
1530.163
1540.398
1550.3
1560.531
1570.258
1580.0646
1590.93
160.108
1600.0421
1610.582
1620.161
1630.611
1640.68
1650.229
1660.0841
1670.0647
1680.817
1690.0429
170.271
180.163
190.0603
20.104
200.307
210.876
220.0896
230.195
240.733
250.579
260.0681
270.356
280.337
290.626
30.935
300.0403
310.354
321.25526e-11
330.768
340.0763
350.722
360.19
370.567
380.81
390.17
40.483
400.224
410.381
420.913
430.306
440.749
450.149
460.322
470.677
480.377
490.367
50.891
500.35
510.328
520.252
530.683
540.435
550.964
560.408
570.738
580.483
590.0599
60.442
600.332
610.882
620.648
630.273
640.387
650.143
660.624
670.864
680.0533
690.139
70.823
700.291
710.623
720.751
730.22
740.563
750.747
760.234
770.0158
780.595
790.148
80.2
800.81
810.784
820.412
830.828
840.771
850.115
860.738
870.417
880.574
890.195
90.352
900.0286
910.196
920.659
930.904
940.852
950.689
960.856
970.5
980.976
990.00259



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: CNhs11335


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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