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FF:11518-119H6: 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:Renal Mesangial 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 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-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-0.125
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-0.09
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: CNhs11333

Jaspar motifP-value
MA0002.20.771
MA0003.10.34
MA0004.10.745
MA0006.10.149
MA0007.10.155
MA0009.10.587
MA0014.10.85
MA0017.10.26
MA0018.20.144
MA0019.10.0936
MA0024.10.539
MA0025.10.827
MA0027.10.468
MA0028.10.102
MA0029.10.377
MA0030.10.343
MA0031.10.127
MA0035.20.0757
MA0038.12.80432e-5
MA0039.20.0853
MA0040.10.293
MA0041.10.257
MA0042.10.761
MA0043.10.0373
MA0046.13.31761e-16
MA0047.20.102
MA0048.10.86
MA0050.17.90881e-6
MA0051.14.09739e-4
MA0052.10.329
MA0055.10.0682
MA0057.10.136
MA0058.10.922
MA0059.10.833
MA0060.14.17789e-6
MA0061.10.898
MA0062.20.00266
MA0065.20.145
MA0066.10.85
MA0067.10.0108
MA0068.10.757
MA0069.10.94
MA0070.10.00327
MA0071.10.668
MA0072.10.97
MA0073.10.823
MA0074.10.261
MA0076.10.00729
MA0077.10.0622
MA0078.10.881
MA0079.20.495
MA0080.21.95336e-6
MA0081.10.0166
MA0083.11.99763e-6
MA0084.10.292
MA0087.10.652
MA0088.10.94
MA0090.10.00115
MA0091.10.671
MA0092.10.997
MA0093.10.811
MA0099.20.00123
MA0100.10.167
MA0101.10.576
MA0102.21.34639e-4
MA0103.10.0274
MA0104.20.288
MA0105.10.572
MA0106.10.178
MA0107.10.952
MA0108.25.98326e-7
MA0111.10.133
MA0112.20.28
MA0113.10.201
MA0114.10.145
MA0115.10.474
MA0116.10.477
MA0117.10.124
MA0119.10.765
MA0122.10.949
MA0124.10.582
MA0125.10.234
MA0131.10.274
MA0135.10.125
MA0136.19.80559e-6
MA0137.20.527
MA0138.20.872
MA0139.10.76
MA0140.10.316
MA0141.10.834
MA0142.10.225
MA0143.10.415
MA0144.10.94
MA0145.10.115
MA0146.10.063
MA0147.10.432
MA0148.10.646
MA0149.10.626
MA0150.10.331
MA0152.10.27
MA0153.11.80008e-8
MA0154.10.611
MA0155.10.0399
MA0156.12.86824e-4
MA0157.10.203
MA0159.10.908
MA0160.10.67
MA0162.10.195
MA0163.10.696
MA0164.10.483
MA0258.10.766
MA0259.10.231



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: CNhs11333

Novel motifP-value
10.0985
100.0239
1000.476
1010.16
1020.537
1030.531
1040.376
1050.161
1060.304
1070.0544
1080.567
1090.473
110.534
1100.565
1110.435
1120.319
1130.85
1140.15
1150.805
1160.615
1170.353
1180.807
1190.997
120.632
1200.81
1210.684
1220.12
1235.66446e-4
1240.486
1250.268
1260.766
1270.376
1280.813
1290.306
130.917
1300.279
1310.378
1320.0757
1330.34
1340.761
1350.964
1360.892
1370.0381
1380.175
1390.557
140.625
1400.69
1410.0433
1420.603
1430.345
1440.865
1450.995
1460.0288
1470.581
1480.073
1490.532
150.284
1500.373
1510.789
1520.0973
1530.103
1540.151
1550.205
1560.339
1570.688
1580.199
1590.967
160.739
1600.116
1610.574
1620.193
1630.69
1640.141
1650.13
1660.877
1670.0595
1680.778
1690.141
170.592
180.859
190.43
20.239
200.613
210.766
220.199
230.688
240.935
250.402
260.401
270.297
280.401
290.397
30.534
300.0319
310.449
320.0233
330.574
340.244
350.0746
360.712
370.541
380.991
390.172
40.421
400.028
410.265
420.577
430.879
440.909
450.164
460.754
470.97
480.687
490.496
50.329
500.351
510.655
520.491
530.341
540.569
550.561
560.272
570.533
580.292
590.0692
60.219
600.933
610.434
620.238
630.632
640.616
650.146
660.119
670.488
680.233
690.168
70.561
700.853
710.509
720.335
730.1
740.261
750.36
760.0254
770.0613
780.636
790.732
80.427
800.801
810.196
820.605
830.803
840.444
850.531
860.518
870.365
880.501
890.309
90.492
900.00265
910.576
920.656
930.455
940.438
950.766
960.557
970.72
980.626
991.58116e-4



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: CNhs11333


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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