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FF:11679-122H5: 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 17:12, 29 March 2012


Name:Renal Mesangial 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 typemesangial cell, intraglomerular
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 numberSC4205
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-penis0.0788
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-0.273
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
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: CNhs12121

Jaspar motifP-value
MA0002.20.832
MA0003.10.309
MA0004.10.584
MA0006.10.17
MA0007.10.144
MA0009.10.631
MA0014.10.968
MA0017.10.122
MA0018.20.233
MA0019.10.0618
MA0024.10.0467
MA0025.10.969
MA0027.10.561
MA0028.10.0147
MA0029.10.229
MA0030.10.486
MA0031.10.0868
MA0035.20.123
MA0038.10.0807
MA0039.20.147
MA0040.10.689
MA0041.10.162
MA0042.10.769
MA0043.10.0325
MA0046.14.34574e-15
MA0047.20.234
MA0048.10.725
MA0050.18.09736e-4
MA0051.10.00633
MA0052.10.175
MA0055.10.128
MA0057.10.245
MA0058.10.606
MA0059.10.944
MA0060.10.0263
MA0061.10.537
MA0062.26.40528e-6
MA0065.20.0932
MA0066.10.533
MA0067.10.082
MA0068.10.886
MA0069.10.897
MA0070.10.00611
MA0071.10.296
MA0072.10.6
MA0073.10.944
MA0074.10.107
MA0076.11.16679e-4
MA0077.10.0724
MA0078.10.755
MA0079.20.396
MA0080.21.4506e-5
MA0081.10.00792
MA0083.14.22292e-4
MA0084.10.274
MA0087.10.732
MA0088.10.779
MA0090.10.00616
MA0091.10.454
MA0092.10.896
MA0093.10.611
MA0099.20.167
MA0100.10.0307
MA0101.10.863
MA0102.20.00475
MA0103.10.00597
MA0104.20.284
MA0105.10.857
MA0106.10.329
MA0107.10.396
MA0108.21.8239e-7
MA0111.10.182
MA0112.20.163
MA0113.10.52
MA0114.10.21
MA0115.10.712
MA0116.10.775
MA0117.10.111
MA0119.10.959
MA0122.10.655
MA0124.10.804
MA0125.10.366
MA0131.10.124
MA0135.10.0265
MA0136.12.88478e-9
MA0137.20.219
MA0138.20.368
MA0139.10.805
MA0140.10.924
MA0141.10.151
MA0142.10.217
MA0143.10.342
MA0144.10.894
MA0145.10.166
MA0146.10.045
MA0147.10.364
MA0148.10.585
MA0149.10.889
MA0150.10.108
MA0152.10.121
MA0153.14.2403e-6
MA0154.10.337
MA0155.10.024
MA0156.12.81689e-6
MA0157.10.0509
MA0159.10.263
MA0160.10.447
MA0162.10.136
MA0163.10.992
MA0164.10.893
MA0258.10.166
MA0259.10.194



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: CNhs12121

Novel motifP-value
10.355
100.0862
1000.25
1010.228
1020.703
1030.67
1040.481
1050.256
1060.0531
1070.00267
1080.373
1090.326
110.414
1100.394
1110.685
1120.726
1130.975
1140.347
1150.121
1160.253
1170.7
1180.796
1190.379
120.903
1200.542
1210.897
1220.331
1230.00486
1240.285
1250.195
1260.741
1270.434
1280.168
1290.0976
130.567
1300.397
1310.35
1320.05
1330.215
1340.966
1350.933
1360.563
1370.00394
1380.189
1390.516
140.658
1400.947
1410.106
1420.565
1430.801
1440.614
1450.355
1460.0795
1470.676
1480.123
1490.423
150.223
1500.331
1510.663
1520.055
1530.0807
1540.222
1550.965
1560.572
1570.328
1580.252
1590.595
160.453
1600.0958
1610.389
1620.0499
1630.526
1640.55
1650.0751
1660.8
1670.17
1680.918
1690.165
170.463
180.85
190.44
20.294
200.78
210.543
220.181
230.518
240.547
250.175
260.374
270.402
280.219
290.604
30.647
300.112
310.34
320.00215
330.727
340.129
350.266
360.624
370.39
380.745
390.312
40.555
400.0242
410.282
420.488
430.911
440.865
450.155
460.639
470.972
480.676
490.581
50.281
500.298
510.387
520.281
530.402
540.381
550.342
560.365
570.511
580.278
590.0419
60.241
600.604
610.589
620.216
630.472
640.398
650.0709
660.583
670.421
680.0393
690.15
70.571
700.622
710.519
720.323
730.0705
740.179
750.727
760.076
770.0201
780.861
790.573
80.297
800.635
810.275
820.696
830.69
840.717
850.814
860.714
870.367
880.354
890.142
90.387
900.00206
910.341
920.813
930.302
940.466
950.434
960.467
970.74
980.914
990.00488



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: CNhs12121


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)
0000066 (epithelial cell)
0000134 (mesenchymal cell)
0000183 (contractile cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000630 (supportive cell)
0000650 (mesangial cell)
0000669 (pericyte cell)
0000723 (somatic stem cell)
0002173 (extraglomerular mesangial cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002518 (kidney epithelial cell)
1000494 (nephron tubule epithelial cell)
1000497 (kidney cell)
1000507 (kidney tubule 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)
0001231 (nephron tubule)
0001285 (nephron)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002303 (juxtaglomerular apparatus)
0002319 (mesangium)
0002321 (extraglomerular mesangium)
0002384 (connective tissue)
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)
0003567 (abdomen connective tissue)
0003586 (trunk connective tissue)
0003838 (abdominal segment connective tissue)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003891 (stroma)
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)
0004211 (nephron epithelium)
0004810 (nephron tubule epithelium)
0004819 (kidney epithelium)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005103 (mesonephric epithelium)
0005169 (interstitial tissue)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005215 (kidney interstitium)
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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