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FF:11532-120A2: 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 16:46, 29 March 2012


Name:Trabecular Meshwork 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
tissueeye
dev stageNA
sexNA
ageNA
cell typetrabecular meshwork cell
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 numberSC6595
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-0.143
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-lymphoma0.161
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: CNhs11340

Jaspar motifP-value
MA0002.20.906
MA0003.10.402
MA0004.10.146
MA0006.10.377
MA0007.10.0134
MA0009.10.379
MA0014.10.792
MA0017.10.571
MA0018.20.00972
MA0019.10.89
MA0024.15.87271e-4
MA0025.10.192
MA0027.10.236
MA0028.10.84
MA0029.10.498
MA0030.10.85
MA0031.10.083
MA0035.20.0978
MA0038.12.15483e-6
MA0039.20.109
MA0040.10.517
MA0041.10.336
MA0042.10.691
MA0043.10.00974
MA0046.10.0016
MA0047.20.6
MA0048.10.132
MA0050.12.15522e-8
MA0051.11.34126e-5
MA0052.10.077
MA0055.18.51397e-5
MA0057.10.364
MA0058.10.412
MA0059.10.265
MA0060.13.99466e-15
MA0061.10.211
MA0062.20.0974
MA0065.20.483
MA0066.10.651
MA0067.10.00778
MA0068.10.779
MA0069.10.633
MA0070.10.00475
MA0071.10.14
MA0072.10.927
MA0073.10.696
MA0074.10.436
MA0076.10.459
MA0077.10.0509
MA0078.10.792
MA0079.20.919
MA0080.21.52236e-4
MA0081.10.103
MA0083.10.17
MA0084.10.279
MA0087.10.469
MA0088.10.107
MA0090.10.212
MA0091.10.0366
MA0092.10.417
MA0093.10.237
MA0099.20.00491
MA0100.10.778
MA0101.10.356
MA0102.20.0116
MA0103.10.125
MA0104.20.61
MA0105.10.55
MA0106.10.397
MA0107.10.0954
MA0108.25.85928e-5
MA0111.10.312
MA0112.20.321
MA0113.10.0221
MA0114.10.505
MA0115.10.984
MA0116.10.919
MA0117.10.317
MA0119.10.35
MA0122.10.981
MA0124.10.0947
MA0125.10.323
MA0131.10.598
MA0135.10.112
MA0136.10.00398
MA0137.20.0468
MA0138.20.814
MA0139.10.727
MA0140.10.183
MA0141.10.203
MA0142.10.89
MA0143.10.467
MA0144.10.273
MA0145.10.7
MA0146.10.0158
MA0147.10.336
MA0148.10.758
MA0149.10.721
MA0150.10.751
MA0152.10.905
MA0153.10.181
MA0154.10.739
MA0155.10.156
MA0156.10.0394
MA0157.10.164
MA0159.10.399
MA0160.10.135
MA0162.10.24
MA0163.10.529
MA0164.10.621
MA0258.10.753
MA0259.10.682



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: CNhs11340

Novel motifP-value
10.527
100.239
1000.708
1010.172
1020.637
1030.287
1040.337
1050.0283
1060.838
1070.441
1080.571
1090.105
110.228
1100.097
1110.361
1120.347
1130.643
1140.244
1150.982
1160.361
1170.977
1180.755
1190.508
120.566
1200.48
1210.309
1220.833
1230.0377
1240.642
1250.375
1260.898
1270.86
1280.821
1290.431
130.47
1300.00712
1310.83
1320.206
1330.0216
1340.426
1350.587
1360.825
1370.165
1380.113
1390.0393
140.924
1400.255
1410.357
1420.568
1430.633
1440.551
1450.386
1460.00695
1470.729
1480.125
1490.865
150.513
1500.368
1510.76
1520.297
1530.172
1540.0436
1550.215
1560.388
1570.425
1580.15
1590.969
160.888
1600.0054
1610.753
1620.0376
1630.437
1640.371
1650.0823
1660.79
1670.165
1680.932
1690.233
170.58
180.518
190.28
20.531
200.693
210.798
220.11
230.741
240.158
250.434
260.211
270.564
280.0574
290.565
30.647
300.0434
310.673
320.0207
330.592
340.104
350.34
360.781
370.823
380.542
390.51
40.341
400.0269
410.464
420.735
430.484
440.158
450.266
460.323
470.492
480.12
490.564
50.221
500.0516
510.457
520.688
530.444
540.489
550.657
560.235
570.696
580.0608
590.183
60.309
600.516
610.791
620.107
630.182
640.0603
650.178
660.0211
670.654
680.00512
690.0359
70.948
700.597
710.492
720.15
730.189
740.593
750.848
760.0999
770.178
780.369
790.628
80.0981
800.852
810.93
820.262
830.662
840.499
850.56
860.528
870.403
880.188
890.511
90.177
900.017
910.423
920.23
930.8
940.763
950.48
960.804
970.655
980.44
991.42904e-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: CNhs11340


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)
0002078 (meso-epithelial cell)
0002321 (embryonic cell)
0002367 (trabecular meshwork cell)
0002371 (somatic cell)

UBERON: Anatomy
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000970 (eye)
0001009 (circulatory system)
0001032 (sensory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001768 (uvea)
0001801 (anterior segment of eyeball)
0002049 (vasculature)
0002104 (visual system)
0002200 (vasculature of head)
0002203 (vasculature of eye)
0003956 (aqueous drainage system)
0004456 (entire sense organ system)
0004535 (cardiovascular system)
0005969 (reticulum trabeculare)
0006876 (vasculature of organ)
0007798 (vascular system)

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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