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FF:11871-125B8: 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 17:33, 29 March 2012


Name:CD14+ monocytes - treated with IFN + N-hexane, donor2
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
sexmale
age51
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD4-2
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-Peripheral0.204
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-0.0335
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.601
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C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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-Whole0.255
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: CNhs13476

Jaspar motifP-value
MA0002.21.75495e-6
MA0003.10.389
MA0004.10.574
MA0006.10.999
MA0007.10.697
MA0009.10.275
MA0014.10.981
MA0017.10.0339
MA0018.20.445
MA0019.10.517
MA0024.10.00165
MA0025.10.0965
MA0027.10.842
MA0028.10.112
MA0029.10.306
MA0030.10.217
MA0031.10.499
MA0035.20.213
MA0038.10.0289
MA0039.20.71
MA0040.10.295
MA0041.10.192
MA0042.10.436
MA0043.16.01875e-4
MA0046.10.0877
MA0047.20.698
MA0048.10.753
MA0050.19.22723e-25
MA0051.12.16002e-15
MA0052.10.648
MA0055.10.667
MA0057.10.82
MA0058.10.346
MA0059.10.548
MA0060.14.97577e-12
MA0061.15.14369e-5
MA0062.20.519
MA0065.20.011
MA0066.10.0696
MA0067.18.69844e-5
MA0068.10.173
MA0069.10.579
MA0070.10.00722
MA0071.10.366
MA0072.10.812
MA0073.10.444
MA0074.10.262
MA0076.10.118
MA0077.10.159
MA0078.10.485
MA0079.20.536
MA0080.21.10409e-14
MA0081.14.65833e-4
MA0083.10.739
MA0084.10.734
MA0087.10.783
MA0088.10.525
MA0090.10.163
MA0091.10.341
MA0092.10.189
MA0093.10.633
MA0099.21.82231e-32
MA0100.10.656
MA0101.10.00233
MA0102.22.60918e-7
MA0103.10.439
MA0104.20.991
MA0105.18.29836e-8
MA0106.10.874
MA0107.13.76798e-4
MA0108.20.00605
MA0111.10.455
MA0112.21.37231e-4
MA0113.10.525
MA0114.10.193
MA0115.10.894
MA0116.12.56478e-4
MA0117.10.238
MA0119.10.333
MA0122.10.859
MA0124.10.827
MA0125.10.426
MA0131.10.458
MA0135.10.382
MA0136.11.4039e-13
MA0137.22.57773e-15
MA0138.20.687
MA0139.10.821
MA0140.10.189
MA0141.10.107
MA0142.10.434
MA0143.10.676
MA0144.12.01577e-6
MA0145.10.237
MA0146.10.1
MA0147.10.952
MA0148.10.979
MA0149.10.277
MA0150.16.18938e-17
MA0152.10.825
MA0153.10.0164
MA0154.10.00317
MA0155.10.919
MA0156.11.5577e-8
MA0157.10.701
MA0159.10.022
MA0160.10.0295
MA0162.10.956
MA0163.12.17649e-7
MA0164.10.595
MA0258.10.00242
MA0259.10.518



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: CNhs13476

Novel motifP-value
10.115
100.0188
1000.837
1010.868
1020.508
1030.346
1040.665
1050.341
1064.2523e-4
1070.164
1080.969
1090.228
110.142
1100.185
1110.0255
1120.253
1130.55
1140.0114
1150.305
1160.785
1170.0655
1180.185
1190.131
120.471
1200.951
1210.549
1220.608
1230.0647
1240.915
1250.395
1260.347
1270.342
1280.0174
1290.506
130.157
1300.131
1310.584
1320.0727
1330.796
1340.614
1350.43
1360.789
1370.0155
1380.133
1390.0647
140.354
1400.297
1410.221
1420.2
1430.0754
1440.711
1450.305
1460.584
1470.284
1480.0285
1490.703
150.132
1500.43
1510.266
1520.0973
1530.647
1540.363
1550.705
1560.575
1570.534
1580.0676
1590.706
160.258
1600.495
1610.466
1620.282
1630.169
1640.154
1650.0641
1660.679
1670.148
1680.422
1690.00853
170.201
180.196
190.298
20.951
200.323
210.315
220.265
230.0372
240.199
250.388
260.0426
270.92
280.449
290.253
30.0574
300.573
310.823
320.929
330.371
340.487
350.212
360.138
370.0719
380.43
390.809
40.956
400.276
410.0414
420.314
430.042
440.605
450.788
460.14
470.45
480.392
490.116
50.232
500.903
510.384
520.236
530.281
540.261
550.301
560.633
570.68
580.0938
590.186
60.772
600.0271
610.544
620.0389
630.382
640.418
650.266
660.243
670.599
680.751
690.723
70.285
700.0202
710.0457
720.141
730.116
740.105
750.106
760.275
770.391
780.0917
790.0288
80.399
800.219
810.329
820.0937
830.311
840.421
850.0104
860.0418
870.65
880.48
890.384
90.354
900.0311
910.257
920.173
930.441
940.0465
950.387
960.394
970.838
980.0838
990.142



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: CNhs13476


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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