FF:11778-124A5: Difference between revisions

Revision as of 19:29, 29 June 2012

Name:	CD41+ megakaryocyte cancer, donor3
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	bone marrow
dev stage	NA
sex	NA
age	NA
cell type	megakaryocyte
cell line	NA
company	NA
collaboration	Hozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	3LL-4
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Download raw sequence, BAM & CTSS

Mm9

BAM	CTSS
[{{{mm9bam}}} download]	[{{{mm9ctss}}} donwload]

Mm10

BAM	CTSS
[{{{mm10bam}}} download]	[{{{mm10ctss}}} 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. Analyst:NA link to dataset. data

CNhs13506

0	0
1	0
10	0
100	0
1000	0.0436
1001	-0.0749
1002	-0.116
1003	-0.102
1004	0
1005	-0.0389
1006	-0.235
1007	-0.318
1008	0
1009	-0.19
101	0.0256
1010	0
1011	0
1012	0
1013	-0.108
1014	-0.0874
1015	-0.222
1016	-0.594
1017	0
1018	0
1019	0
102	0
1020	0.386
1021	0.38
1022	-0.16
1023	0
1024	-0.307
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0887
1030	0
1031	-0.911
1032	-0.184
1033	-0.0752
1034	0
1035	0
1036	0.47
1037	0
1038	-0.475
1039	-0.348
104	0
1040	-0.718
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data no result for this sample

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs13506

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0237
MA0003.1	MA0003.1	0.344
MA0004.1	MA0004.1	0.5
MA0006.1	MA0006.1	0.757
MA0007.1	MA0007.1	0.847
MA0009.1	MA0009.1	0.538
MA0014.1	MA0014.1	0.924
MA0017.1	MA0017.1	0.176
MA0018.2	MA0018.2	0.306
MA0019.1	MA0019.1	0.521
MA0024.1	MA0024.1	2.21887e-8
MA0025.1	MA0025.1	0.246
MA0027.1	MA0027.1	0.566
MA0028.1	MA0028.1	0.0289
MA0029.1	MA0029.1	0.485
MA0030.1	MA0030.1	0.366
MA0031.1	MA0031.1	0.837
MA0035.2	MA0035.2	1.9254e-5
MA0038.1	MA0038.1	0.986
MA0039.2	MA0039.2	0.995
MA0040.1	MA0040.1	0.212
MA0041.1	MA0041.1	0.758
MA0042.1	MA0042.1	0.63
MA0043.1	MA0043.1	0.132
MA0046.1	MA0046.1	4.04355e-5
MA0047.2	MA0047.2	0.974
MA0048.1	MA0048.1	0.0963
MA0050.1	MA0050.1	0.189
MA0051.1	MA0051.1	0.257
MA0052.1	MA0052.1	9.70639e-5
MA0055.1	MA0055.1	0.0287
MA0057.1	MA0057.1	0.661
MA0058.1	MA0058.1	0.5
MA0059.1	MA0059.1	0.0616
MA0060.1	MA0060.1	0.0132
MA0061.1	MA0061.1	0.0585
MA0062.2	MA0062.2	0.00168
MA0065.2	MA0065.2	0.0788
MA0066.1	MA0066.1	0.105
MA0067.1	MA0067.1	0.64
MA0068.1	MA0068.1	0.31
MA0069.1	MA0069.1	0.356
MA0070.1	MA0070.1	0.291
MA0071.1	MA0071.1	0.437
MA0072.1	MA0072.1	0.814
MA0073.1	MA0073.1	0.954
MA0074.1	MA0074.1	0.688
MA0076.1	MA0076.1	0.0925
MA0077.1	MA0077.1	0.465
MA0078.1	MA0078.1	0.831
MA0079.2	MA0079.2	0.0186
MA0080.2	MA0080.2	4.42372e-4
MA0081.1	MA0081.1	0.47
MA0083.1	MA0083.1	0.0122
MA0084.1	MA0084.1	0.531
MA0087.1	MA0087.1	0.214
MA0088.1	MA0088.1	0.0793
MA0090.1	MA0090.1	0.0975
MA0091.1	MA0091.1	0.113
MA0092.1	MA0092.1	0.84
MA0093.1	MA0093.1	0.591
MA0099.2	MA0099.2	0.616
MA0100.1	MA0100.1	0.00618
MA0101.1	MA0101.1	0.144
MA0102.2	MA0102.2	0.833
MA0103.1	MA0103.1	0.611
MA0104.2	MA0104.2	0.203
MA0105.1	MA0105.1	1.1806e-4
MA0106.1	MA0106.1	0.365
MA0107.1	MA0107.1	0.337
MA0108.2	MA0108.2	0.0224
MA0111.1	MA0111.1	0.916
MA0112.2	MA0112.2	0.0152
MA0113.1	MA0113.1	0.37
MA0114.1	MA0114.1	0.341
MA0115.1	MA0115.1	0.305
MA0116.1	MA0116.1	0.00578
MA0117.1	MA0117.1	0.542
MA0119.1	MA0119.1	0.259
MA0122.1	MA0122.1	0.45
MA0124.1	MA0124.1	0.973
MA0125.1	MA0125.1	0.063
MA0131.1	MA0131.1	0.494
MA0135.1	MA0135.1	0.298
MA0136.1	MA0136.1	0.00835
MA0137.2	MA0137.2	0.746
MA0138.2	MA0138.2	0.0546
MA0139.1	MA0139.1	0.357
MA0140.1	MA0140.1	1.29776e-25
MA0141.1	MA0141.1	0.0409
MA0142.1	MA0142.1	0.301
MA0143.1	MA0143.1	0.295
MA0144.1	MA0144.1	0.856
MA0145.1	MA0145.1	0.714
MA0146.1	MA0146.1	0.306
MA0147.1	MA0147.1	0.123
MA0148.1	MA0148.1	0.709
MA0149.1	MA0149.1	0.0187
MA0150.1	MA0150.1	0.00424
MA0152.1	MA0152.1	0.181
MA0153.1	MA0153.1	0.0101
MA0154.1	MA0154.1	0.0441
MA0155.1	MA0155.1	0.418
MA0156.1	MA0156.1	0.0239
MA0157.1	MA0157.1	0.931
MA0159.1	MA0159.1	0.0234
MA0160.1	MA0160.1	0.264
MA0162.1	MA0162.1	0.389
MA0163.1	MA0163.1	3.12106e-4
MA0164.1	MA0164.1	0.274
MA0258.1	MA0258.1	0.0651
MA0259.1	MA0259.1	0.409

FANTOM5 phase1 novel unique motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs13506

Novel motif	Logo	P-value
1	1	0.0728
10	10	0.022
100	100	0.344
101	101	0.799
102	102	0.71
103	103	0.00572
104	104	0.922
105	105	0.799
106	106	0.456
107	107	0.833
108	108	0.987
109	109	0.0555
11	11	0.154
110	110	0.0766
111	111	0.034
112	112	0.0277
113	113	0.743
114	114	0.307
115	115	0.95
116	116	0.635
117	117	7.41646e-4
118	118	0.112
119	119	0.372
12	12	0.867
120	120	0.981
121	121	0.311
122	122	0.662
123	123	0.273
124	124	0.239
125	125	0.091
126	126	0.199
127	127	0.334
128	128	0.499
129	129	0.407
13	13	0.00899
130	130	0.66
131	131	0.657
132	132	0.232
133	133	0.762
134	134	0.136
135	135	0.29
136	136	0.878
137	137	0.362
138	138	0.61
139	139	0.467
14	14	0.889
140	140	0.408
141	141	0.816
142	142	0.362
143	143	0.309
144	144	0.985
145	145	0.0313
146	146	0.962
147	147	0.839
148	148	0.488
149	149	0.675
15	15	0.0535
150	150	0.34
151	151	0.536
152	152	0.334
153	153	0.891
154	154	0.758
155	155	0.191
156	156	4.86729e-82
157	157	0.901
158	158	0.0337
159	159	0.572
160	160	0.623
161	161	0.0466
162	162	0.824
163	163	0.496
164	164	0.017
165	165	0.48
166	166	0.251
167	167	0.0283
168	168	0.875
169	169	0.36
17	17	0.436
18	18	0.0771
19	19	0.734
2	2	0.208
20	20	0.0191
21	21	0.284
22	22	0.862
23	23	0.22
24	24	0.638
25	25	0.213
26	26	0.00343
27	27	0.828
28	28	0.418
29	29	0.00632
3	3	0.0557
30	30	0.515
31	31	0.73
32	32	0.709
33	33	0.11
34	34	0.668
35	35	0.394
36	36	0.0171
37	37	0.151
38	38	0.589
39	39	0.952
4	4	0.881
40	40	0.124
41	41	0.314
42	42	0.117
43	43	0.198
44	44	0.471
45	45	0.5
46	46	0.139
47	47	0.173
48	48	0.313
49	49	0.0937
5	5	0.00553
50	50	0.834
51	51	0.719
52	52	0.839
53	53	0.525
54	54	0.728
55	55	0.0747
56	56	0.664
57	57	0.167
58	58	0.485
59	59	0.455
6	6	0.702
60	60	0.493
61	61	0.553
62	62	0.177
63	63	0.564
64	64	0.614
65	65	0.698
66	66	0.189
67	67	0.337
68	68	0.279
69	69	0.926
7	7	0.0756
70	70	0.128
71	71	0.0129
72	72	0.355
73	73	0.313
74	74	0.566
75	75	0.0194
76	76	0.123
77	77	0.993
78	78	0.0472
79	79	0.618
8	8	0.0193
80	80	0.0728
81	81	0.607
82	82	0.555
83	83	0.379
84	84	0.875
85	85	0.577
86	86	0.542
87	87	0.691
88	88	0.741
89	89	0.611
9	9	0.939
90	90	0.0466
91	91	0.181
92	92	0.478
93	93	0.572
94	94	0.188
95	95	0.135
96	96	0.163
97	97	0.975
98	98	0.548
99	99	0.488

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown. Analyst:NA library id: CNhs13506

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011131 mouse CD41-positive megakaryocyte cancer sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000988 (hematopoietic cell)
0000839 (myeloid lineage restricted progenitor cell)
0000548 (animal cell)
0000034 (stem cell)
0002032 (hematopoietic oligopotent progenitor cell)
0000763 (myeloid cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0000037 (hematopoietic stem cell)
0000050 (megakaryocyte-erythroid progenitor cell)
0000553 (megakaryocyte progenitor cell)
0000556 (megakaryocyte)
0000566 (angioblastic mesenchymal cell)
0000049 (common myeloid progenitor)
0000837 (hematopoietic multipotent progenitor cell)
0002027 (CD9-positive, CD41-positive megakaryocyte cell)
0002006 (Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell)
0002024 (Kit-positive megakaryocyte progenitor cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002371 (bone marrow)
0001474 (bone element)
0002384 (connective tissue)
0000926 (mesoderm)
0000479 (tissue)
0000062 (organ)
0004765 (skeletal element)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)
0003081 (lateral plate mesoderm)
0006603 (presumptive mesoderm)
0003061 (blood island)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
NA

@@ Line 6: / Line 6: @@
 |created_by=
 |creation_date=
+|datafreeze_phase=1
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!2.55!356.78!Klf1;;chr2:28477452..28477483,-!p1@Gfi1b!2.28!234.35!Gfi1b;;chr15:103085660..103085681,-!p1@Nfe2!2.25!258.84!Nfe2;;chr4:114732112..114732158,+!p1@Tal1!2.22!346.98!Tal1;;chr7:122989594..122989626,-!p1@Sox6!2.12!129.42!Sox6;;chrX:7544943..7545001,-!p1@Gata1!2.10!124.52!Gata1;;chr4:135728581..135728668,+!p1@E2f2!2.05!502.29!E2f2;;chr9:96159147..96159204,+!p2@Tfdp2!2.03!191.68!Tfdp2;;chr15:103085690..103085710,-!p3@Nfe2!1.95!95.14!Nfe2;;chr7:122989632..122989668,-!p2@Sox6!1.91!79.75!Sox6;;chr15:103082088..103082136,-!p2@Nfe2!1.84!68.56!Nfe2;;chr11:11584970..11585030,+!p2@Ikzf1!1.79!85.35!Ikzf1;;chr10:88145766..88145770,-!p1@Spic!1.78!76.25!Spic;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.76!71.36!Zbtb11;;chr8:87225670..87225697,+!p2@Lyl1!1.64!118.93!Lyl1;;chr9:96159116..96159130,+!p6@Tfdp2!1.57!44.77!Tfdp2;;chr9:96159225..96159249,+!p5@Tfdp2!1.48!32.18!Tfdp2;;chr4:135728473..135728494,+!p5@E2f2!1.41!24.48!E2f2;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!1.39!32.88!Carhsp1;;chr4:87452200..87452229,-!p2@Mllt3!1.36!45.47!Mllt3;;chr9:96159210..96159221,+!p10@Tfdp2!1.36!21.69!Tfdp2;;chr5:65203599..65203617,+!p8@Klf3!1.34!34.28!Klf3;;chr8:87225702..87225726,+!p3@Lyl1!1.31!39.18!Lyl1;;chr9:96159133..96159145,+!p9@Tfdp2!1.31!19.59!Tfdp2;;chr8:124806048..124806094,+!p1@Zfpm1!1.30!168.59!Zfpm1;;chr11:11585912..11585950,+!p6@Ikzf1!1.30!23.79!Ikzf1;;chr13:112476264..112476282,+!p3@Mier3!1.29!25.88!Mier3;;chr4:114729957..114730012,+!p3@Tal1!1.28!18.19!Tal1;;chr4:135728181..135728203,+!p2@E2f2!1.27!23.09!E2f2;;chr8:124806017..124806040,+!p2@Zfpm1!1.26!183.98!Zfpm1;;chr15:103085802..103085817,-!p4@Nfe2!1.22!19.59!Nfe2;;chr9:51021788..51021802,+!p1@Pou2af1!1.18!16.79!Pou2af1;;chr15:103083245..103083260,-!p7@Nfe2!1.18!13.99!Nfe2;;chr2:162880387..162880413,+!p1@Mybl2!1.16!83.95!Mybl2;;chr2:162880327..162880385,+!p2@Mybl2!1.14!84.65!Mybl2;;chr7:56136362..56136400,-!p1@E2f8!1.14!83.25!E2f8;;chr11:120491440..120491474,-!p3@Mafg!1.14!18.89!Mafg;;chr10:79884592..79884621,-!p5@Tcf3!1.13!12.59!Tcf3;;chr6:86619130..86619158,-!p2@Mxd1!1.08!160.20!Mxd1;;chr10:126727842..126727859,+!p1@Ddit3!1.07!307.11!Ddit3;;chr16:92826249..92826325,-!p1@Runx1!1.07!26.58!Runx1;;chr4:135728282..135728310,+!p4@E2f2!1.06!11.89!E2f2;;chr13:55431084..55431137,-!p1@Mxd3!1.05!81.15!Mxd3;;chr14:47896467..47896523,-!p1@Wdhd1!1.02!117.53!Wdhd1;;chr5:104183477..104183548,+!p6@Aff1!1.02!18.89!Aff1;;chrX:137135036..137135064,-!p4@Tsc22d3!1.02!18.89!Tsc22d3;;chr10:80598968..80599012,+!p5@Zbtb7a!1.02!12.59!Zbtb7a;;chr7:122989676..122989687,-!p8@Sox6!1.00!9.09!Sox6;;chr5:140267476..140267493,+!p1@Mafk!0.99!50.37!Mafk;;chr5:65194720..65194738,+!p2@Klf3!0.97!46.17!Klf3;;chr1:38721792..38721845,-!p1@Aff3!0.97!10.49!Aff3;;chr4:87452180..87452196,-!p3@Mllt3!0.95!16.09!Mllt3;;chr4:44723559..44723593,-!p1@Pax5!0.94!7.70!Pax5;;chr4:114732159..114732166,+!p6@Tal1!0.94!7.70!Tal1;;chr13:112476296..112476308,+!p4@Mier3!0.92!8.39!Mier3;;chr7:148452314..148452329,-!p1@Irf7!0.89!49.67!Irf7;;chr9:96159427..96159432,+!p11@Tfdp2!0.87!7.70!Tfdp2;;chr11:101413151..101413207,-!p1@Brca1!0.86!63.66!Brca1;;chr6:86619104..86619119,-!p1@Mxd1!0.86!54.57!Mxd1;;chr5:65203575..65203589,+!p11@Klf3!0.86!7.70!Klf3;;chr4:135728311..135728342,+!p3@E2f2!0.86!6.30!E2f2;;chr15:103085864..103085876,-!p5@Nfe2!0.86!6.30!Nfe2;;chr17:56970481..56970551,-!p2@Rfx2!0.84!19.59!Rfx2;;chr10:20880629..20880683,-!p1@Myb!0.83!17.49!Myb;;chr18:70727922..70728052,+!p1@Mbd2!0.82!215.47!Mbd2;;chr4:114730015..114730042,+!p7@Tal1!0.82!5.60!Tal1;;chr4:87452236..87452249,-!p9@Mllt3!0.82!5.60!Mllt3;;chr8:107821563..107821642,+!p1@E2f4!0.81!167.20!E2f4;;chr14:56223010..56223067,+!p1@Irf9!0.80!45.47!Irf9;;chr10:41995430..41995458,-!p3@Foxo3!0.80!14.69!Foxo3;;chr7:56136974..56136989,-!p4@E2f8!0.80!9.09!E2f8;;chr4:114730254..114730276,+!p2@Tal1!0.80!7.00!Tal1;;chr11:23980664..23980706,+!p2@Bcl11a!0.78!23.79!Bcl11a;;chr17:56970339..56970428,-!p1@Rfx2!0.78!16.79!Rfx2;;chr10:30522881..30522960,-!p1@Ncoa7!0.77!64.36!Ncoa7;;chr10:30522690..30522752,-!p2@Ncoa7!0.77!32.18!Ncoa7;;chr14:79881330..79881415,+!p3@Elf1!0.77!17.49!Elf1;;chr14:32978944..32978953,+!p8@Gm6768,p8@Ncoa4!0.77!4.90!Ncoa4;;chr2:166868994..166869023,-!p7@Znfx1!0.77!4.90!Znfx1;;chr15:80085920..80085941,+!p1@Atf4!0.76!598.13!Atf4;;chr19:53384965..53384984,+!p4@Mxi1!0.76!14.69!Mxi1;;chr6:99216488..99216534,-!p2@Foxp1!0.76!14.69!Foxp1;;chr5:65194709..65194716,+!p10@Klf3!0.76!9.79!Klf3;;chr13:59924433..59924504,-!p1@Zcchc6!0.75!114.73!Zcchc6;;chr5:104183219..104183236,+!p2@Aff1!0.75!34.98!Aff1;;chr13:64254457..64254497,-!p1@Zfp367!0.75!22.39!Zfp367;;chr11:11585678..11585745,+!p5@Ikzf1!0.75!7.00!Ikzf1;;chr5:65213356..65213412,+!p6@Klf3!0.73!9.79!Klf3;;chr7:56136402..56136420,-!p3@E2f8!0.73!8.39!E2f8;;chr4:102792009..102792021,+!p6@Mier1!0.72!7.70!Mier1;;chr13:30841099..30841116,+!p1@Irf4!0.72!7.00!Irf4;;chr2:162880418..162880429,+!p4@Mybl2!0.72!5.60!Mybl2;;chr4:44723633..44723646,-!p3@Pax5!0.72!4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FF:11778-124A5: Difference between revisions

From FANTOM5_SSTAR

Revision as of 19:29, 29 June 2012

CNhs13506

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0