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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000075,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001444,UBERON:0001456,UBERON:0001474,UBERON:0001704,UBERON:0001708,UBERON:0001709,UBERON:0002050,UBERON:0002090,UBERON:0002204,UBERON:0002244,UBERON:0002329,UBERON:0002342,UBERON:0002346,UBERON:0002384,UBERON:0002397,UBERON:0002514,UBERON:0002532,UBERON:0002539,UBERON:0003059,UBERON:0003075,UBERON:0003077,UBERON:0003089,UBERON:0003104,UBERON:0003129,UBERON:0003323,UBERON:0003457,UBERON:0003462,UBERON:0004066,UBERON:0004068,UBERON:0004089,UBERON:0004120,UBERON:0004121,UBERON:0004288,UBERON:0004765,UBERON:0005291,UBERON:0005423,UBERON:0005620,UBERON:0005705,UBERON:0005944,UBERON:0006598,UBERON:0007284,UBERON:0007375,UBERON:0008001,UBERON:0008193,UBERON:0008814,UBERON:0008816,UBERON:0009142,UBERON:0009292
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000075,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001444,UBERON:0001456,UBERON:0001474,UBERON:0001704,UBERON:0001708,UBERON:0001709,UBERON:0002050,UBERON:0002090,UBERON:0002204,UBERON:0002244,UBERON:0002329,UBERON:0002342,UBERON:0002346,UBERON:0002384,UBERON:0002397,UBERON:0002514,UBERON:0002532,UBERON:0002539,UBERON:0003059,UBERON:0003075,UBERON:0003077,UBERON:0003089,UBERON:0003104,UBERON:0003129,UBERON:0003323,UBERON:0003457,UBERON:0003462,UBERON:0004066,UBERON:0004068,UBERON:0004089,UBERON:0004120,UBERON:0004121,UBERON:0004288,UBERON:0004765,UBERON:0005291,UBERON:0005423,UBERON:0005620,UBERON:0005705,UBERON:0005944,UBERON:0006598,UBERON:0007284,UBERON:0007375,UBERON:0008001,UBERON:0008193,UBERON:0008814,UBERON:0008816,UBERON:0009142,UBERON:0009292
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669

Revision as of 16:59, 29 March 2012


Name:normal embryonic palatal mesenchymal cell line:HEPM
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepalate
dev stageNA
sexfemale
agefetal
cell typeunclassifiable
cell lineHEPM
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.124
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-0.00192
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs11894

Jaspar motifP-value
MA0002.23.60456e-4
MA0003.10.808
MA0004.10.0325
MA0006.10.983
MA0007.10.855
MA0009.10.227
MA0014.10.37
MA0017.14.50755e-4
MA0018.20.313
MA0019.10.829
MA0024.10.218
MA0025.10.0302
MA0027.10.767
MA0028.10.00257
MA0029.10.944
MA0030.10.484
MA0031.10.028
MA0035.20.00585
MA0038.10.644
MA0039.20.00176
MA0040.10.828
MA0041.10.561
MA0042.10.958
MA0043.10.406
MA0046.10.0228
MA0047.20.228
MA0048.10.0217
MA0050.17.68724e-4
MA0051.10.0883
MA0052.10.647
MA0055.10.765
MA0057.10.399
MA0058.12.02926e-4
MA0059.10.0165
MA0060.10.00506
MA0061.10.00207
MA0062.21.07048e-10
MA0065.20.00274
MA0066.10.356
MA0067.10.699
MA0068.10.287
MA0069.10.162
MA0070.10.525
MA0071.10.469
MA0072.10.449
MA0073.10.547
MA0074.10.403
MA0076.10.00182
MA0077.10.355
MA0078.10.806
MA0079.20.283
MA0080.25.18637e-11
MA0081.10.0148
MA0083.10.0184
MA0084.10.149
MA0087.10.897
MA0088.10.051
MA0090.10.0119
MA0091.10.117
MA0092.10.759
MA0093.10.0275
MA0099.21.57952e-5
MA0100.10.841
MA0101.12.05747e-4
MA0102.20.379
MA0103.10.00392
MA0104.22.30987e-4
MA0105.10.0661
MA0106.10.751
MA0107.12.29844e-4
MA0108.20.102
MA0111.10.622
MA0112.20.684
MA0113.10.69
MA0114.16.35056e-4
MA0115.10.0304
MA0116.10.0909
MA0117.10.447
MA0119.10.484
MA0122.10.0374
MA0124.10.0274
MA0125.10.398
MA0131.10.767
MA0135.10.428
MA0136.13.74997e-15
MA0137.20.25
MA0138.20.437
MA0139.10.486
MA0140.10.0486
MA0141.10.28
MA0142.10.0618
MA0143.10.794
MA0144.10.344
MA0145.10.933
MA0146.10.177
MA0147.10.00134
MA0148.10.184
MA0149.10.288
MA0150.15.29199e-4
MA0152.10.0151
MA0153.10.578
MA0154.10.0572
MA0155.10.0654
MA0156.11.15354e-12
MA0157.10.145
MA0159.10.172
MA0160.10.059
MA0162.10.269
MA0163.10.549
MA0164.10.941
MA0258.10.515
MA0259.10.433



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: CNhs11894

Novel motifP-value
10.219
100.667
1000.754
1010.73
1020.338
1030.36
1040.846
1050.262
1060.482
1070.418
1080.737
1090.234
110.911
1100.509
1110.214
1120.678
1130.557
1140.631
1152.33578e-4
1160.355
1170.244
1180.694
1190.287
120.262
1200.271
1210.396
1220.0126
1230.0496
1240.631
1250.399
1260.294
1270.477
1280.604
1290.18
130.247
1300.879
1310.891
1320.032
1330.812
1340.177
1350.0779
1360.732
1370.119
1380.539
1390.364
140.107
1400.0941
1410.291
1420.271
1430.596
1440.231
1450.576
1460.145
1470.239
1480.152
1490.313
150.0594
1500.581
1510.274
1520.037
1530.614
1540.814
1550.731
1560.33
1570.319
1580.0211
1590.603
160.169
1600.915
1610.575
1620.918
1630.225
1640.526
1650.245
1660.017
1670.631
1680.171
1690.482
170.635
180.983
190.0214
20.998
200.809
210.634
220.766
230.611
240.215
250.188
260.658
270.57
280.213
290.609
30.392
300.901
310.74
329.46976e-17
331
340.209
350.619
360.0747
370.426
380.151
390.736
40.299
400.0289
410.149
420.324
430.393
440.192
450.255
460.649
470.175
480.512
490.175
50.489
500.938
510.59
520.831
530.123
540.995
550.271
560.541
570.549
580.0815
590.991
60.507
600.58
610.549
620.252
630.945
640.847
650.825
660.0704
670.485
680.957
690.623
70.13
700.298
710.395
720.662
730.324
740.971
750.382
760.998
770.898
780.0345
790.00717
80.556
800.0491
810.961
820.776
830.389
840.96
850.318
860.751
870.84
880.477
890.557
90.738
900.304
910.967
920.804
930.418
940.791
950.967
960.952
970.682
980.0614
990.165



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: CNhs11894


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000075 (subdivision of skeletal system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001444 (subdivision of head)
0001456 (face)
0001474 (bone element)
0001708 (jaw skeleton)
0001709 (upper jaw region)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002244 (premaxilla)
0002329 (somite)
0002342 (neural crest)
0002346 (neurectoderm)
0002384 (connective tissue)
0002397 (maxilla)
0002514 (intramembranous bone)
0002532 (epiblast (generic))
0002539 (pharyngeal arch)
0003059 (presomitic mesoderm)
0003075 (neural plate)
0003077 (paraxial mesoderm)
0003089 (sclerotome)
0003104 (mesenchyme)
0003129 (skull)
0003323 (mesenchyme of upper jaw)
0003457 (head bone)
0003462 (facial bone)
0004066 (frontonasal prominence)
0004068 (medial nasal prominence)
0004089 (midface)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004288 (skeleton)
0004765 (skeletal element)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005620 (primary palate)
0005705 (primary palate mesenchyme)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
0007375 (roof of mouth)
0008001 (irregular bone)
0008193 (pneumatized bone)
0008814 (pharyngeal arch system)
0008816 (embryonic head)
0009142 (entire embryonic mesenchyme)
0009292 (embryonic nasal process)

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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