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FF:11510-119G7: 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:Alveolar Epithelial 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
tissuelung
dev stageNA
sexNA
ageNA
cell typeepithelial cell of lung, small airway
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:5020
catalog numberSC3205
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-0.117
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-lymphoma0.053
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs11325

Jaspar motifP-value
MA0002.20.848
MA0003.10.372
MA0004.10.745
MA0006.10.184
MA0007.10.029
MA0009.10.68
MA0014.10.79
MA0017.10.0876
MA0018.20.181
MA0019.10.29
MA0024.10.791
MA0025.10.605
MA0027.10.536
MA0028.10.309
MA0029.10.0839
MA0030.10.319
MA0031.10.0617
MA0035.20.00345
MA0038.10.259
MA0039.20.0923
MA0040.10.458
MA0041.10.554
MA0042.10.503
MA0043.10.0269
MA0046.10.00335
MA0047.20.375
MA0048.10.851
MA0050.11.98854e-10
MA0051.17.32045e-6
MA0052.10.329
MA0055.10.072
MA0057.10.149
MA0058.10.362
MA0059.10.549
MA0060.10.00975
MA0061.10.802
MA0062.20.0107
MA0065.20.0102
MA0066.10.354
MA0067.10.00441
MA0068.10.764
MA0069.10.805
MA0070.10.0609
MA0071.10.262
MA0072.10.799
MA0073.10.864
MA0074.10.679
MA0076.10.0689
MA0077.10.229
MA0078.10.408
MA0079.20.946
MA0080.25.57889e-4
MA0081.10.0297
MA0083.11.14006e-9
MA0084.10.0734
MA0087.10.729
MA0088.10.608
MA0090.17.56676e-5
MA0091.10.763
MA0092.10.253
MA0093.10.674
MA0099.25.78459e-11
MA0100.10.229
MA0101.10.864
MA0102.20.0464
MA0103.11.51521e-5
MA0104.20.646
MA0105.10.897
MA0106.10.0636
MA0107.10.871
MA0108.22.25875e-14
MA0111.10.782
MA0112.20.0348
MA0113.10.273
MA0114.10.0315
MA0115.10.157
MA0116.10.57
MA0117.10.24
MA0119.10.0677
MA0122.10.889
MA0124.10.157
MA0125.10.0688
MA0131.10.173
MA0135.10.191
MA0136.10.0181
MA0137.20.156
MA0138.20.999
MA0139.10.421
MA0140.10.183
MA0141.10.175
MA0142.10.734
MA0143.10.179
MA0144.10.883
MA0145.10.0372
MA0146.10.114
MA0147.10.928
MA0148.10.191
MA0149.10.255
MA0150.10.416
MA0152.10.438
MA0153.10.0436
MA0154.10.253
MA0155.10.121
MA0156.10.152
MA0157.10.22
MA0159.10.0701
MA0160.10.243
MA0162.10.114
MA0163.10.703
MA0164.10.762
MA0258.10.261
MA0259.10.885



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: CNhs11325

Novel motifP-value
10.983
100.259
1000.938
1010.123
1020.959
1030.32
1040.649
1050.075
1060.0284
1070.0146
1080.578
1090.0243
110.308
1100.184
1110.433
1120.593
1130.958
1140.78
1150.918
1160.157
1170.845
1180.8
1190.489
120.931
1200.393
1210.24
1220.245
1230.062
1240.872
1250.34
1260.41
1270.779
1280.184
1290.173
130.251
1300.216
1310.877
1320.224
1330.307
1340.443
1350.291
1360.419
1370.155
1380.358
1390.806
140.88
1400.988
1410.4
1420.718
1430.334
1440.372
1450.214
1460.0329
1470.974
1480.185
1490.114
150.386
1500.342
1510.543
1520.0503
1530.681
1540.343
1550.4
1560.139
1570.524
1580.676
1590.81
160.218
1600.0366
1610.641
1620.0998
1630.568
1640.356
1650.18
1660.587
1670.0715
1680.758
1690.119
170.225
180.154
190.486
20.193
200.613
210.993
220.295
230.29
240.226
250.793
260.188
270.373
280.414
290.863
30.932
300.0696
310.75
320.451
330.208
340.246
350.249
360.987
370.41
380.323
390.109
40.257
400.00328
410.967
420.694
430.367
440.863
450.227
460.398
470.587
480.391
490.506
50.757
500.224
510.507
520.244
530.668
540.626
550.635
560.264
570.662
580.839
590.0596
60.546
600.298
610.367
620.796
630.176
640.312
650.119
660.128
670.454
680.236
690.017
70.364
700.897
710.495
720.664
730.0591
740.161
750.955
760.178
770.00204
780.719
790.708
80.194
800.752
810.377
820.627
830.717
840.641
850.85
860.813
870.205
880.24
890.131
90.687
900.0279
910.317
920.789
930.822
940.922
950.122
960.933
970.615
980.491
990.00165



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: CNhs11325


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)
0000082 (epithelial cell of lung)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000322 (pneumocyte)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002202 (epithelial cell of tracheobronchial tree)
0002321 (embryonic cell)
0002368 (respiratory epithelial cell)
0002371 (somatic cell)
0002632 (epithelial cell of lower respiratory tract)

UBERON: Anatomy
0000025 (tube)
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000115 (lung epithelium)
0000117 (respiratory tube)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
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)
0000487 (simple squamous epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001558 (lower respiratory tract)
0002048 (lung)
0002050 (embryonic structure)
0002169 (alveolar sac)
0002224 (thoracic cavity)
0002299 (alveolus of lung)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003215 (alveolus)
0003258 (endoderm of foregut)
0003914 (epithelial tube)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004802 (respiratory tract epithelium)
0004807 (respiratory system epithelium)
0004821 (pulmonary alveolus epithelium)
0004894 (alveolar wall)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0006524 (alveolar system)
0006914 (squamous epithelium)
0007026 (primitive gut)
0007196 (tracheobronchial tree)
0007499 (epithelial sac)
0008874 (pulmonary acinus)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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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