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FF:11675-122H1: 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 17:23, 29 March 2012


Name:Renal Glomerular Endothelial Cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexNA
ageNA
cell typeendothelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number5993
catalog numberSC4005
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-penis0
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-lymphoma0.383
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: CNhs12624

Jaspar motifP-value
MA0002.21.90509e-4
MA0003.10.741
MA0004.10.559
MA0006.10.0446
MA0007.10.393
MA0009.10.806
MA0014.10.829
MA0017.10.579
MA0018.23.80378e-5
MA0019.10.0618
MA0024.14.43733e-5
MA0025.10.127
MA0027.10.742
MA0028.10.0762
MA0029.10.953
MA0030.10.041
MA0031.10.0138
MA0035.20.969
MA0038.10.108
MA0039.20.558
MA0040.10.87
MA0041.10.313
MA0042.10.649
MA0043.16.68524e-8
MA0046.10.0069
MA0047.20.42
MA0048.10.28
MA0050.10.141
MA0051.10.797
MA0052.10.338
MA0055.10.404
MA0057.10.352
MA0058.10.225
MA0059.10.679
MA0060.10.0113
MA0061.10.0478
MA0062.26.1234e-4
MA0065.20.503
MA0066.10.98
MA0067.17.81451e-4
MA0068.10.587
MA0069.10.021
MA0070.10.714
MA0071.10.714
MA0072.10.349
MA0073.10.974
MA0074.10.603
MA0076.10.00136
MA0077.15.38846e-4
MA0078.10.0334
MA0079.20.198
MA0080.20.241
MA0081.10.866
MA0083.10.57
MA0084.10.247
MA0087.10.553
MA0088.10.151
MA0090.10.162
MA0091.10.5
MA0092.10.973
MA0093.10.525
MA0099.20.627
MA0100.10.591
MA0101.10.508
MA0102.28.41938e-6
MA0103.10.0111
MA0104.20.0406
MA0105.10.548
MA0106.10.013
MA0107.10.166
MA0108.20.12
MA0111.10.981
MA0112.20.175
MA0113.10.99
MA0114.10.181
MA0115.10.24
MA0116.10.457
MA0117.10.188
MA0119.10.45
MA0122.10.855
MA0124.10.823
MA0125.10.948
MA0131.10.327
MA0135.10.488
MA0136.10.116
MA0137.20.294
MA0138.20.849
MA0139.10.958
MA0140.10.881
MA0141.10.486
MA0142.10.963
MA0143.10.6
MA0144.10.679
MA0145.10.868
MA0146.10.0226
MA0147.10.232
MA0148.10.356
MA0149.10.162
MA0150.10.181
MA0152.10.461
MA0153.10.489
MA0154.10.22
MA0155.10.353
MA0156.10.842
MA0157.10.258
MA0159.10.383
MA0160.10.0769
MA0162.10.0632
MA0163.10.204
MA0164.10.97
MA0258.10.0346
MA0259.10.507



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: CNhs12624

Novel motifP-value
10.37
100.239
1000.299
1010.164
1020.81
1030.518
1040.994
1050.0992
1060.381
1070.0336
1080.75
1090.587
110.829
1100.582
1110.436
1120.571
1130.342
1140.36
1150.521
1160.81
1170.0622
1180.715
1190.881
120.0506
1200.00892
1210.944
1220.361
1230.00184
1240.0561
1250.995
1260.998
1270.481
1280.874
1290.895
130.466
1300.454
1310.0734
1320.364
1330.792
1340.415
1350.974
1360.0451
1370.11
1380.977
1390.00975
140.29
1400.892
1410.707
1420.261
1430.487
1440.834
1450.603
1460.823
1470.0409
1480.498
1490.821
150.274
1500.0548
1510.244
1520.0125
1530.198
1540.861
1550.148
1560.428
1570.0421
1580.0641
1590.546
160.812
1600.138
1610.673
1620.246
1630.4
1640.442
1650.876
1660.544
1670.148
1680.182
1690.635
170.735
180.874
190.987
20.843
200.533
210.942
220.292
230.861
240.448
250.651
260.843
270.862
280.254
290.494
30.362
300.788
310.479
320.711
330.842
340.858
350.022
360.743
370.893
380.717
390.149
40.553
400.656
410.852
420.728
430.0831
440.0371
450.841
460.985
470.825
480.922
490.0216
50.556
500.927
510.869
520.368
530.0326
540.608
550.267
560.785
570.867
580.12
590.449
60.281
600.171
610.652
620.212
630.859
640.437
650.725
660.363
670.73
680.338
690.604
70.295
700.0203
710.236
720.735
730.0628
740.819
750.239
760.17
770.617
780.834
790.334
80.446
800.432
810.422
820.136
830.555
840.00651
850.185
860.396
870.646
880.38
890.916
90.89
900.103
910.597
920.504
930.428
940.623
950.996
960.581
970.591
980.184
990.00597



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: CNhs12624


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)
0000666 (fenestrated cell)
0002078 (meso-epithelial cell)
0002188 (glomerular endothelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000025 (tube)
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000074 (renal glomerulus)
0000080 (mesonephros)
0000083 (mesonephric tubule)
0000119 (cell layer)
0000464 (anatomical space)
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)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001008 (renal system)
0001062 (anatomical entity)
0001225 (cortex of kidney)
0001229 (renal corpuscle)
0001230 (glomerular capsule)
0001285 (nephron)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003060 (pronephric duct)
0003064 (intermediate mesoderm)
0003074 (mesonephric duct)
0003081 (lateral plate mesoderm)
0003103 (compound organ)
0003104 (mesenchyme)
0003220 (metanephric mesenchyme)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003914 (epithelial tube)
0003918 (kidney mesenchyme)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004198 (comma-shaped body)
0004199 (S-shaped body)
0004208 (nephrogenic mesenchyme)
0004209 (renal vesicle)
0004819 (kidney epithelium)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005103 (mesonephric epithelium)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005721 (pronephric mesoderm)
0005749 (glomerular tuft)
0005754 (rostral part of nephrogenic cord)
0006553 (renal duct)
0006554 (urinary system structure)
0006555 (excretory tube)
0007684 (uriniferous tubule)
0007687 (kidney field)
0009142 (entire embryonic mesenchyme)
0009201 (nephric duct)

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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