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FF:11861-125A7: 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 - treated with IFN + N-hexane, 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 numberD3-2
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-Peripheral0.124
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-0.0994
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.561
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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-Whole0.22
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: CNhs13466

Jaspar motifP-value
MA0002.26.29055e-8
MA0003.10.306
MA0004.10.646
MA0006.10.862
MA0007.10.597
MA0009.10.621
MA0014.10.917
MA0017.10.0109
MA0018.20.904
MA0019.10.776
MA0024.10.00149
MA0025.10.12
MA0027.10.731
MA0028.10.128
MA0029.10.363
MA0030.10.235
MA0031.10.567
MA0035.20.271
MA0038.10.0142
MA0039.20.934
MA0040.10.144
MA0041.10.87
MA0042.10.884
MA0043.10.015
MA0046.10.207
MA0047.20.631
MA0048.10.997
MA0050.12.72741e-26
MA0051.14.65789e-17
MA0052.10.767
MA0055.10.415
MA0057.10.844
MA0058.10.457
MA0059.10.631
MA0060.11.86972e-12
MA0061.19.6733e-5
MA0062.20.543
MA0065.20.0083
MA0066.10.0735
MA0067.10.00124
MA0068.10.944
MA0069.10.538
MA0070.19.43768e-4
MA0071.10.375
MA0072.10.83
MA0073.10.34
MA0074.10.174
MA0076.10.145
MA0077.10.199
MA0078.10.469
MA0079.20.625
MA0080.24.51743e-15
MA0081.13.13034e-4
MA0083.10.696
MA0084.10.963
MA0087.10.694
MA0088.10.625
MA0090.10.163
MA0091.10.184
MA0092.10.202
MA0093.10.719
MA0099.28.33567e-29
MA0100.10.779
MA0101.10.00214
MA0102.23.99937e-7
MA0103.10.605
MA0104.20.731
MA0105.14.28901e-7
MA0106.10.962
MA0107.14.22157e-4
MA0108.20.00241
MA0111.10.445
MA0112.27.41105e-5
MA0113.10.384
MA0114.10.148
MA0115.10.539
MA0116.13.3652e-4
MA0117.10.308
MA0119.10.339
MA0122.10.805
MA0124.10.983
MA0125.10.511
MA0131.10.368
MA0135.10.594
MA0136.11.10099e-14
MA0137.24.67606e-17
MA0138.20.833
MA0139.10.891
MA0140.10.236
MA0141.10.0712
MA0142.10.533
MA0143.10.581
MA0144.14.92254e-7
MA0145.10.181
MA0146.10.0957
MA0147.10.72
MA0148.10.937
MA0149.10.283
MA0150.12.76296e-13
MA0152.10.697
MA0153.10.00701
MA0154.10.00266
MA0155.10.799
MA0156.18.59996e-9
MA0157.10.627
MA0159.10.0132
MA0160.10.0408
MA0162.10.632
MA0163.16.72317e-7
MA0164.10.718
MA0258.10.00174
MA0259.10.508



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: CNhs13466

Novel motifP-value
10.108
100.0282
1000.817
1010.795
1020.532
1030.145
1040.625
1050.521
1066.10285e-4
1070.177
1080.793
1090.152
110.1
1100.189
1110.0316
1120.263
1130.652
1140.00777
1150.365
1160.721
1170.0568
1180.215
1190.153
120.471
1200.332
1210.696
1220.582
1230.184
1240.923
1250.37
1260.394
1270.273
1280.0103
1290.384
130.18
1300.199
1310.568
1320.0825
1330.936
1340.606
1350.346
1360.87
1370.0196
1380.167
1390.0561
140.381
1400.253
1410.304
1420.274
1430.0175
1440.781
1450.278
1460.866
1470.361
1480.013
1490.618
150.116
1500.42
1510.307
1520.0816
1530.565
1540.487
1550.481
1560.647
1570.945
1580.172
1590.421
160.236
1600.368
1610.485
1620.428
1630.148
1640.168
1650.0456
1660.767
1670.24
1680.269
1690.00888
170.166
180.145
190.256
20.97
200.433
210.35
220.23
230.0302
240.208
250.347
260.0384
270.706
280.511
290.242
30.0532
300.675
310.754
320.737
330.344
340.464
350.195
360.168
370.0818
380.448
390.738
40.965
400.308
410.0342
420.316
430.0404
440.563
450.724
460.12
470.365
480.357
490.125
50.221
500.878
510.296
520.198
530.45
540.253
550.229
560.645
570.781
580.0909
590.132
60.64
600.0203
610.71
620.0287
630.351
640.411
650.257
660.339
670.555
680.879
690.525
70.267
700.0142
710.0363
720.106
730.125
740.0486
750.0876
760.372
770.322
780.0698
790.0349
80.31
800.156
810.302
820.0512
830.218
840.353
850.0153
860.0741
870.347
880.516
890.207
90.248
900.0543
910.367
920.125
930.609
940.0437
950.329
960.387
970.856
980.0924
990.213



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: CNhs13466


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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