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FF:11514-119H2: 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 17:10, 29 March 2012


Name:Renal Glomerular Endothelial Cells, donor1
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 numberlot:5952
catalog numberSC4005
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-0.107
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-0.12
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
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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: CNhs12074

Jaspar motifP-value
MA0002.20.391
MA0003.10.195
MA0004.10.436
MA0006.10.213
MA0007.10.0557
MA0009.10.983
MA0014.10.858
MA0017.10.0424
MA0018.20.00172
MA0019.10.172
MA0024.10.0741
MA0025.10.395
MA0027.10.482
MA0028.16.96783e-4
MA0029.10.373
MA0030.10.311
MA0031.10.131
MA0035.28.81939e-4
MA0038.10.246
MA0039.20.509
MA0040.10.198
MA0041.10.207
MA0042.10.656
MA0043.15.14762e-5
MA0046.10.0249
MA0047.20.16
MA0048.10.806
MA0050.10.132
MA0051.10.452
MA0052.10.0679
MA0055.10.393
MA0057.10.249
MA0058.10.353
MA0059.10.625
MA0060.10.0396
MA0061.10.397
MA0062.28.75993e-6
MA0065.20.0227
MA0066.10.167
MA0067.10.131
MA0068.10.207
MA0069.10.353
MA0070.10.37
MA0071.10.0474
MA0072.10.331
MA0073.10.614
MA0074.10.203
MA0076.17.8585e-6
MA0077.13.05838e-4
MA0078.10.0135
MA0079.20.311
MA0080.20.0809
MA0081.10.965
MA0083.10.808
MA0084.10.8
MA0087.10.426
MA0088.10.803
MA0090.10.219
MA0091.10.192
MA0092.10.437
MA0093.10.433
MA0099.20.00108
MA0100.10.2
MA0101.10.257
MA0102.25.51132e-4
MA0103.10.176
MA0104.20.484
MA0105.10.547
MA0106.10.0166
MA0107.10.153
MA0108.20.00343
MA0111.10.876
MA0112.20.0321
MA0113.10.15
MA0114.10.206
MA0115.10.751
MA0116.10.461
MA0117.10.14
MA0119.10.0864
MA0122.10.176
MA0124.10.695
MA0125.10.989
MA0131.10.239
MA0135.10.123
MA0136.10.232
MA0137.20.0875
MA0138.20.0492
MA0139.10.249
MA0140.10.0236
MA0141.10.00229
MA0142.10.926
MA0143.10.978
MA0144.10.528
MA0145.10.116
MA0146.10.0733
MA0147.10.649
MA0148.10.0362
MA0149.10.0785
MA0150.10.356
MA0152.10.473
MA0153.10.6
MA0154.10.12
MA0155.10.0109
MA0156.10.202
MA0157.10.65
MA0159.10.0808
MA0160.10.0714
MA0162.10.0846
MA0163.10.149
MA0164.10.195
MA0258.10.0552
MA0259.10.263



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: CNhs12074

Novel motifP-value
10.548
100.684
1000.728
1010.342
1020.546
1030.778
1040.393
1050.207
1060.0382
1070.0542
1080.446
1090.147
110.0357
1100.0975
1110.592
1120.359
1130.743
1140.395
1150.922
1160.711
1170.826
1180.866
1190.139
120.501
1200.428
1210.947
1220.74
1230.224
1240.591
1250.562
1260.572
1270.96
1280.157
1290.0128
130.467
1300.705
1310.0511
1320.14
1330.205
1340.82
1350.128
1360.84
1370.515
1380.713
1390.243
140.817
1400.711
1410.139
1420.535
1430.00404
1440.332
1450.161
1460.101
1470.304
1480.691
1490.0184
150.34
1500.23
1510.446
1520.0264
1530.259
1540.383
1550.633
1560.116
1570.555
1580.698
1590.805
160.57
1600.00247
1610.751
1620.465
1630.825
1640.887
1650.286
1660.245
1670.165
1680.419
1690.031
170.122
180.318
190.072
20.22
200.718
210.858
220.0818
230.0494
240.749
250.745
260.0868
270.146
280.416
290.852
30.519
300.449
310.434
320.196
330.327
340.0839
350.686
360.161
370.234
380.172
390.231
40.168
400.00775
410.0744
420.807
430.292
440.26
450.169
460.0796
470.449
480.091
490.366
50.633
500.559
510.292
520.503
530.955
540.489
550.981
560.503
570.421
580.821
590.0118
60.206
600.205
610.973
620.804
630.329
640.0875
650.0186
660.585
670.805
680.0562
690.142
70.643
700.145
710.392
720.637
730.0204
740.858
750.337
760.355
770.0365
780.729
790.00733
80.0277
800.805
810.9
820.269
830.822
840.131
850.0782
860.788
870.415
880.653
890.417
90.262
900.665
910.0638
920.385
930.719
940.455
950.0785
960.513
970.633
980.0664
990.0476



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: CNhs12074


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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