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FF:11863-125A9: 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 17:32, 29 March 2012


Name:CD14+ monocytes - mock treated, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
age69
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD3-4
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-Peripheral0.111
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-0.0576
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.39
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.493
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.289
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: CNhs13468

Jaspar motifP-value
MA0002.21.94898e-7
MA0003.10.307
MA0004.10.595
MA0006.10.714
MA0007.10.819
MA0009.10.34
MA0014.10.953
MA0017.10.0301
MA0018.20.861
MA0019.10.524
MA0024.19.63139e-4
MA0025.10.0938
MA0027.10.908
MA0028.10.482
MA0029.10.511
MA0030.10.706
MA0031.10.905
MA0035.20.405
MA0038.10.00753
MA0039.20.891
MA0040.10.52
MA0041.10.267
MA0042.10.844
MA0043.10.0298
MA0046.10.034
MA0047.20.683
MA0048.10.913
MA0050.11.80443e-4
MA0051.10.1
MA0052.10.682
MA0055.10.518
MA0057.10.754
MA0058.10.395
MA0059.10.666
MA0060.11.30206e-12
MA0061.10.00233
MA0062.20.0853
MA0065.20.024
MA0066.10.0706
MA0067.10.0035
MA0068.10.231
MA0069.10.69
MA0070.10.0304
MA0071.10.251
MA0072.10.584
MA0073.10.4
MA0074.10.189
MA0076.10.447
MA0077.10.13
MA0078.10.427
MA0079.20.724
MA0080.23.32684e-16
MA0081.12.94943e-4
MA0083.10.477
MA0084.10.733
MA0087.10.662
MA0088.10.845
MA0090.10.094
MA0091.10.411
MA0092.10.268
MA0093.10.632
MA0099.21.30783e-31
MA0100.10.603
MA0101.10.0553
MA0102.22.23278e-6
MA0103.10.817
MA0104.20.742
MA0105.16.04377e-6
MA0106.10.765
MA0107.10.0196
MA0108.29.19071e-5
MA0111.10.279
MA0112.25.25176e-5
MA0113.10.959
MA0114.10.226
MA0115.10.737
MA0116.11.58646e-4
MA0117.10.375
MA0119.10.391
MA0122.10.979
MA0124.10.49
MA0125.10.403
MA0131.10.527
MA0135.10.974
MA0136.11.16391e-17
MA0137.20.731
MA0138.20.998
MA0139.10.864
MA0140.10.287
MA0141.10.0813
MA0142.10.774
MA0143.10.562
MA0144.10.385
MA0145.10.202
MA0146.10.0458
MA0147.10.711
MA0148.10.947
MA0149.10.223
MA0150.19.44132e-12
MA0152.10.331
MA0153.10.00165
MA0154.10.0033
MA0155.10.634
MA0156.12.02556e-9
MA0157.10.557
MA0159.10.0265
MA0160.10.0451
MA0162.10.718
MA0163.11.06814e-6
MA0164.10.751
MA0258.10.00153
MA0259.10.4



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: CNhs13468

Novel motifP-value
10.109
100.0192
1000.753
1010.6
1020.47
1030.24
1040.679
1050.392
1060.00132
1070.147
1080.899
1090.173
110.128
1100.299
1110.0273
1120.22
1130.57
1140.0125
1150.381
1160.629
1170.0283
1180.184
1190.132
120.429
1200.888
1210.703
1220.814
1230.0154
1240.599
1250.395
1260.281
1270.233
1280.0194
1290.518
130.2
1300.123
1310.666
1320.144
1330.992
1340.521
1350.337
1360.996
1370.0047
1380.139
1390.0248
140.383
1400.0913
1410.436
1420.901
1430.0339
1440.772
1450.353
1460.47
1470.327
1480.018
1490.499
150.13
1500.468
1510.284
1520.0856
1530.309
1540.468
1550.283
1560.791
1570.37
1580.114
1590.932
160.312
1600.45
1610.686
1620.576
1630.531
1640.0991
1650.139
1660.472
1670.214
1680.562
1690.0075
170.167
180.184
190.196
20.862
200.391
210.204
220.185
230.0768
240.27
250.38
260.0232
270.748
280.465
290.246
30.0463
300.568
310.67
320.761
330.483
340.345
350.141
360.196
370.0699
380.316
390.661
40.923
400.184
410.0238
420.351
430.0481
440.691
450.713
460.0978
470.389
480.334
490.101
50.203
500.926
510.312
520.317
530.223
540.255
550.291
560.599
570.68
580.101
590.114
60.515
600.0443
610.391
620.0369
630.38
640.414
650.209
660.239
670.59
680.892
690.734
70.309
700.0107
710.0298
720.252
730.0806
740.0922
750.0598
760.259
770.319
780.0906
790.0398
80.258
800.328
810.324
820.0751
830.483
840.532
850.0122
860.0516
870.436
880.449
890.311
90.347
900.0538
910.316
920.158
930.429
940.0288
950.256
960.327
970.975
980.149
990.185



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: CNhs13468


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)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000860 (classical monocyte)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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