FF:1350-25C3: Difference between revisions

Latest revision as of 19:00, 4 June 2020

Name:	bone (os femoris), neonate N20
Species:	Mouse (Mus musculus)
Library ID:	CNhs11195
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	bone (os femoris)
dev stage	20 days neonate
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004931

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11195		CAGE		DRX008939		DRR009813

Accession ID Mm9

Library id		BAM		CTSS
CNhs11195		DRZ001238		DRZ002621

Accession ID Mm10

Library id		BAM		CTSS
CNhs11195		DRZ012588		DRZ013971

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	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

CNhs11195

0	0
1	0
10	0
100	0
1000	0.535
1001	0.304
1002	-0.0587
1003	0.116
1004	0
1005	0.172
1006	0.368
1007	0.0791
1008	0
1009	0.2
101	0.00531
1010	0
1011	0
1012	0
1013	-0.118
1014	0.207
1015	-0.182
1016	-0.072
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.172
1022	0.522
1023	0
1024	0.172
1025	0
1026	0
1027	0
1028	0
1029	0.0728
103	1.192
1030	0.39
1031	0.0306
1032	0.0115
1033	0.00808
1034	0
1035	0.172
1036	0.163
1037	0
1038	-0.113
1039	0.0859
104	0
1040	0.0576
1041	0.172

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

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: CNhs11195

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00741
MA0003.1	MA0003.1	0.0732
MA0004.1	MA0004.1	0.323
MA0006.1	MA0006.1	0.0902
MA0007.1	MA0007.1	0.668
MA0009.1	MA0009.1	0.443
MA0014.1	MA0014.1	0.744
MA0017.1	MA0017.1	0.792
MA0018.2	MA0018.2	4.83997e-4
MA0019.1	MA0019.1	0.247
MA0024.1	MA0024.1	0.19
MA0025.1	MA0025.1	0.121
MA0027.1	MA0027.1	0.0906
MA0028.1	MA0028.1	0.0682
MA0029.1	MA0029.1	0.571
MA0030.1	MA0030.1	0.566
MA0031.1	MA0031.1	0.456
MA0035.2	MA0035.2	0.426
MA0038.1	MA0038.1	0.0424
MA0039.2	MA0039.2	0.591
MA0040.1	MA0040.1	0.498
MA0041.1	MA0041.1	0.106
MA0042.1	MA0042.1	0.592
MA0043.1	MA0043.1	0.00939
MA0046.1	MA0046.1	1.95212e-6
MA0047.2	MA0047.2	0.438
MA0048.1	MA0048.1	0.92
MA0050.1	MA0050.1	0.647
MA0051.1	MA0051.1	0.803
MA0052.1	MA0052.1	1.27095e-5
MA0055.1	MA0055.1	0.326
MA0057.1	MA0057.1	0.334
MA0058.1	MA0058.1	0.22
MA0059.1	MA0059.1	0.464
MA0060.1	MA0060.1	0.0589
MA0061.1	MA0061.1	0.107
MA0062.2	MA0062.2	0.0166
MA0065.2	MA0065.2	0.18
MA0066.1	MA0066.1	0.235
MA0067.1	MA0067.1	0.184
MA0068.1	MA0068.1	0.422
MA0069.1	MA0069.1	0.331
MA0070.1	MA0070.1	0.665
MA0071.1	MA0071.1	0.885
MA0072.1	MA0072.1	0.75
MA0073.1	MA0073.1	0.806
MA0074.1	MA0074.1	0.979
MA0076.1	MA0076.1	0.0169
MA0077.1	MA0077.1	0.43
MA0078.1	MA0078.1	0.323
MA0079.2	MA0079.2	0.0676
MA0080.2	MA0080.2	0.00702
MA0081.1	MA0081.1	0.426
MA0083.1	MA0083.1	0.0988
MA0084.1	MA0084.1	0.814
MA0087.1	MA0087.1	0.477
MA0088.1	MA0088.1	0.752
MA0090.1	MA0090.1	0.717
MA0091.1	MA0091.1	0.151
MA0092.1	MA0092.1	0.521
MA0093.1	MA0093.1	0.268
MA0099.2	MA0099.2	0.702
MA0100.1	MA0100.1	0.732
MA0101.1	MA0101.1	0.901
MA0102.2	MA0102.2	0.791
MA0103.1	MA0103.1	0.0102
MA0104.2	MA0104.2	0.152
MA0105.1	MA0105.1	0.00169
MA0106.1	MA0106.1	0.435
MA0107.1	MA0107.1	0.815
MA0108.2	MA0108.2	0.493
MA0111.1	MA0111.1	0.648
MA0112.2	MA0112.2	1.84616e-7
MA0113.1	MA0113.1	0.883
MA0114.1	MA0114.1	0.391
MA0115.1	MA0115.1	0.302
MA0116.1	MA0116.1	0.00488
MA0117.1	MA0117.1	0.874
MA0119.1	MA0119.1	0.106
MA0122.1	MA0122.1	0.707
MA0124.1	MA0124.1	0.929
MA0125.1	MA0125.1	0.355
MA0131.1	MA0131.1	0.931
MA0135.1	MA0135.1	0.0936
MA0136.1	MA0136.1	0.896
MA0137.2	MA0137.2	0.0406
MA0138.2	MA0138.2	0.846
MA0139.1	MA0139.1	0.832
MA0140.1	MA0140.1	9.46226e-9
MA0141.1	MA0141.1	0.0762
MA0142.1	MA0142.1	0.904
MA0143.1	MA0143.1	0.371
MA0144.1	MA0144.1	0.49
MA0145.1	MA0145.1	0.229
MA0146.1	MA0146.1	0.644
MA0147.1	MA0147.1	0.308
MA0148.1	MA0148.1	0.503
MA0149.1	MA0149.1	0.342
MA0150.1	MA0150.1	0.232
MA0152.1	MA0152.1	0.0214
MA0153.1	MA0153.1	1.58027e-6
MA0154.1	MA0154.1	0.00411
MA0155.1	MA0155.1	0.503
MA0156.1	MA0156.1	0.819
MA0157.1	MA0157.1	0.706
MA0159.1	MA0159.1	0.15
MA0160.1	MA0160.1	0.6
MA0162.1	MA0162.1	0.149
MA0163.1	MA0163.1	2.12311e-5
MA0164.1	MA0164.1	0.961
MA0258.1	MA0258.1	8.20917e-4
MA0259.1	MA0259.1	0.852

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: CNhs11195

Novel motif	Logo	P-value
1	1	0.0937
10	10	0.0733
100	100	0.537
101	101	0.871
102	102	0.891
103	103	0.167
104	104	0.627
105	105	0.288
106	106	0.0854
107	107	0.115
108	108	0.905
109	109	0.0794
11	11	0.223
110	110	0.197
111	111	0.349
112	112	0.381
113	113	0.909
114	114	0.388
115	115	0.931
116	116	0.446
117	117	0.117
118	118	0.399
119	119	0.804
12	12	0.841
120	120	0.519
121	121	0.895
122	122	0.893
123	123	0.534
124	124	0.195
125	125	0.394
126	126	0.374
127	127	0.137
128	128	0.164
129	129	0.827
13	13	0.0137
130	130	0.608
131	131	0.713
132	132	0.539
133	133	0.772
134	134	0.874
135	135	0.78
136	136	0.195
137	137	0.4
138	138	0.566
139	139	0.765
14	14	0.876
140	140	0.18
141	141	0.335
142	142	0.757
143	143	0.174
144	144	0.15
145	145	0.363
146	146	0.903
147	147	0.993
148	148	0.416
149	149	0.92
15	15	0.418
150	150	0.408
151	151	0.202
152	152	0.271
153	153	0.975
154	154	0.864
155	155	0.651
156	156	0
157	157	0.629
158	158	0.724
159	159	0.381
160	160	0.0752
161	161	0.766
162	162	0.754
163	163	0.455
164	164	0.24
165	165	0.742
166	166	0.957
167	167	0.411
168	168	0.844
169	169	0.00298
17	17	0.268
18	18	0.785
19	19	0.041
2	2	0.606
20	20	0.268
21	21	0.5
22	22	0.454
23	23	0.646
24	24	0.816
25	25	0.507
26	26	0.0073
27	27	0.75
28	28	0.512
29	29	0.22
3	3	0.0849
30	30	0.636
31	31	0.425
32	32	0.00169
33	33	0.961
34	34	0.365
35	35	0.709
36	36	0.878
37	37	0.0661
38	38	0.0662
39	39	0.616
4	4	0.856
40	40	0.686
41	41	0.937
42	42	0.361
43	43	0.184
44	44	0.619
45	45	0.651
46	46	0.0635
47	47	0.373
48	48	0.544
49	49	0.33
5	5	6.92008e-5
50	50	0.281
51	51	0.733
52	52	0.286
53	53	0.68
54	54	0.675
55	55	0.912
56	56	0.297
57	57	0.531
58	58	0.768
59	59	0.0142
6	6	0.672
60	60	0.143
61	61	0.708
62	62	0.279
63	63	0.203
64	64	0.699
65	65	0.17
66	66	0.515
67	67	0.123
68	68	0.649
69	69	0.584
7	7	0.0859
70	70	0.359
71	71	0.0156
72	72	0.959
73	73	0.219
74	74	0.899
75	75	0.213
76	76	0.764
77	77	0.737
78	78	0.015
79	79	0.87
8	8	0.155
80	80	0.328
81	81	0.411
82	82	0.562
83	83	0.594
84	84	0.371
85	85	0.0366
86	86	0.766
87	87	0.131
88	88	0.39
89	89	0.551
9	9	0.464
90	90	0.958
91	91	0.231
92	92	0.311
93	93	0.792
94	94	0.453
95	95	0.393
96	96	0.745
97	97	0.706
98	98	0.681
99	99	0.658

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: CNhs11195

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011467 mouse bone- os femoris - neonate N20 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000981 (femur)
0001474 (bone element)
0000479 (tissue)
0011216 (organ system subdivision)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0002472 (stylopod)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0006058 (multi-limb segment region)
0003608 (hindlimb long bone)
0003826 (upper leg bone)
0008202 (bone of hip region)
0000075 (subdivision of skeletal system)
0004381 (skeleton of limb)
0007273 (pelvic appendage skeleton)
0004765 (skeletal element)
0010912 (subdivision of skeleton)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002513 (endochondral bone)
0004375 (bone of free limb or fin)
0010740 (bone of appendage girdle complex)
0002529 (limb segment)
0010363 (endochondral element)
0010538 (paired limb/fin segment)
0002428 (limb bone)
0010742 (bone of pelvic complex)
0002495 (long bone)
0003464 (hindlimb bone)
0003606 (limb long bone)
0005893 (leg bone)
0010317 (germ layer / neural crest derived structure)
0010712 (limb skeleton subdivision)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000978 (leg)
0002103 (hindlimb)
0000376 (hindlimb stylopod)
0001441 (hindlimb skeleton)
0011249 (appendicular skeletal system)
0000154 (posterior region of body)
0010709 (pelvic complex)
0002091 (appendicular skeleton)
0004288 (skeleton)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011467 (mouse bone- os femoris - neonate N20 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0005866 (pre-cartilage condensation)
UBERON:0006234 (femur pre-cartilage condensation)
UBERON:0010316 (germ layer / neural crest)
UBERON:0010882 (limb bone pre-cartilage condensation)
UBERON:0010886 (hindlimb bone pre-cartilage condensation)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004931
+|accession_numbers=CAGE;DRX008939;DRR009813;DRZ001238;DRZ002621;DRZ012588;DRZ013971
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000981,UBERON:0001474,UBERON:0000479,UBERON:0011216,UBERON:0000062,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0002472,UBERON:0008784,UBERON:0001062,UBERON:0000480,UBERON:0006058,UBERON:0003608,UBERON:0003826,UBERON:0008202,UBERON:0000075,UBERON:0004381,UBERON:0007273,UBERON:0004765,UBERON:0010912,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0002513,UBERON:0004375,UBERON:0010740,UBERON:0002529,UBERON:0010363,UBERON:0010538,UBERON:0002428,UBERON:0010742,UBERON:0002495,UBERON:0003464,UBERON:0003606,UBERON:0005893,UBERON:0010317,UBERON:0010712,UBERON:0010758,UBERON:0010707,UBERON:0002204,UBERON:0001434,UBERON:0000978,UBERON:0002103,UBERON:0000376,UBERON:0001441,UBERON:0011249,UBERON:0000154,UBERON:0010709,UBERON:0002091,UBERON:0004288
 |ancestors_in_cell_lineage_facet=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!1.86!72.25!Klf1;;chr7:122989594..122989626,-!p1@Sox6!1.84!67.40!Sox6;;chr2:28477452..28477483,-!p1@Gfi1b!1.76!69.34!Gfi1b;;chr7:122989632..122989668,-!p2@Sox6!1.69!48.49!Sox6;;chr13:83643159..83643226,+!p3@Mef2c!1.64!42.18!Mef2c;;chr4:44723559..44723593,-!p1@Pax5!1.63!41.21!Pax5;;chr15:103085660..103085681,-!p1@Nfe2!1.61!58.67!Nfe2;;chr9:51021788..51021802,+!p1@Pou2af1!1.58!44.12!Pou2af1;;chr15:102197405..102197454,-!p1@Sp7!1.55!34.43!Sp7;;chr9:96159147..96159204,+!p2@Tfdp2!1.54!61.58!Tfdp2;;chr1:38721792..38721845,-!p1@Aff3!1.54!41.70!Aff3;;chr4:114732112..114732158,+!p1@Tal1!1.53!70.31!Tal1;;chr17:44951553..44951586,-!p2@Runx2!1.53!36.37!Runx2;;chr3:99057269..99057306,+!p1@Tbx15!1.43!31.52!Tbx15;;chr7:51787434..51787448,-!p1@Spib!1.41!34.91!Spib;;chr13:30841099..30841116,+!p1@Irf4!1.40!37.82!Irf4;;chrX:7544943..7545001,-!p1@Gata1!1.40!24.24!Gata1;;chr11:100683839..100683890,-!p2@Stat5b!1.36!50.91!Stat5b;;chr2:120365588..120365602,-!p2@Zfp106!1.34!34.43!Zfp106;;chr15:103082088..103082136,-!p2@Nfe2!1.33!20.36!Nfe2;;chr1:57028125..57028149,-!p2@Satb2!1.32!19.88!Satb2;;chr4:44723520..44723544,-!p2@Pax5!1.32!19.88!Pax5;;chr3:99057677..99057730,+!p2@Tbx15!1.31!19.40!Tbx15;;chr17:44951431..44951445,-!p3@Runx2!1.31!19.40!Runx2;;chr11:11584970..11585030,+!p2@Ikzf1!1.29!26.18!Ikzf1;;chr15:102196745..102196769,-!p2@Sp7!1.29!18.43!Sp7;;chr4:87452200..87452229,-!p2@Mllt3!1.23!33.94!Mllt3;;chr4:44723633..44723646,-!p3@Pax5!1.23!16.00!Pax5;;chr1:57029281..57029326,-!p1@Satb2!1.21!23.76!Satb2;;chr11:94981424..94981439,+!p1@Dlx3!1.21!17.46!Dlx3;;chr6:6832076..6832092,-!p1@Dlx5!1.20!17.46!Dlx5;;chr7:119885539..119885574,+!p3@Tead1!1.20!15.03!Tead1;;chr12:74147689..74147711,-!p1@Six1!1.18!30.55!Six1;;chr16:92826249..92826325,-!p1@Runx1!1.17!33.46!Runx1;;chr6:99216488..99216534,-!p2@Foxp1!1.15!37.34!Foxp1;;chr9:96159116..96159130,+!p6@Tfdp2!1.15!16.49!Tfdp2;;chr10:106931775..106931798,-!p1@Myf6!1.15!13.09!Myf6;;chr4:135728181..135728203,+!p2@E2f2!1.13!16.49!E2f2;;chr11:11586218..11586285,+!p1@Ikzf1!1.11!38.31!Ikzf1;;chr1:57028556..57028583,-!p5@Satb2!1.10!11.64!Satb2;;chr17:14011485..14011507,+!p2@Mllt4!1.10!11.64!Mllt4;;chr4:135728581..135728668,+!p1@E2f2!1.09!54.79!E2f2;;chr10:20880731..20880775,-!p2@Myb!1.07!22.79!Myb;;chr15:103085690..103085710,-!p3@Nfe2!1.07!11.64!Nfe2;;chr18:80909801..80909819,-!p1@Nfatc1!1.05!61.09!Nfatc1;;chr1:57028538..57028553,-!p6@Satb2!1.05!10.18!Satb2;;chr5:20361092..20361119,-!p4@Phtf2!1.03!9.70!Phtf2;;chr15:97738692..97738747,-!p1@Vdr!1.02!53.34!Vdr;;chr4:32325445..32325468,+!p4@Bach2!1.02!13.58!Bach2;;chr10:79884592..79884621,-!p5@Tcf3!1.01!9.21!Tcf3;;chr6:52190467..52190500,-!p1@Hoxa10!1.01!9.21!Hoxa10;;chr11:44430812..44430838,+!p1@Ebf1!0.99!87.28!Ebf1;;chr16:43363190..43363242,+!p2@Zbtb20!0.99!27.64!Zbtb20;;chr10:20880698..20880717,-!p3@Myb!0.99!14.06!Myb;;chr9:96159225..96159249,+!p5@Tfdp2!0.97!9.21!Tfdp2;;chr4:87452180..87452196,-!p3@Mllt3!0.95!16.00!Mllt3;;chr11:11585912..11585950,+!p6@Ikzf1!0.95!10.18!Ikzf1;;chr6:6831950..6831985,-!p2@Dlx5!0.95!8.73!Dlx5;;chr12:34642510..34642530,+!p1@Twist1!0.94!25.21!Twist1;;chr4:32325955..32325971,+!p3@Bach2!0.94!10.18!Bach2;;chr9:96159133..96159145,+!p9@Tfdp2!0.94!7.76!Tfdp2;;chr11:98407234..98407259,-!p2@Ikzf3!0.94!7.76!Ikzf3;;chr11:16908650..16908690,-!p1@Plek!0.92!46.55!Plek;;chr15:102196790..102196799,-!p3@Sp7!0.92!7.27!Sp7;;chr13:83643136..83643158,+!p7@Mef2c!0.92!7.27!Mef2c;;chr1:169548377..169548430,+!p1@Rxrg!0.92!7.27!Rxrg;;chr6:6831928..6831949,-!p3@Dlx5!0.92!7.27!Dlx5;;chr1:165243792..165243808,-!p1@Prrx1!0.88!24.24!Prrx1;;chr8:87225670..87225697,+!p2@Lyl1!0.88!19.88!Lyl1;;chr10:88145766..88145770,-!p1@Spic!0.86!8.24!Spic;;chr11:98407264..98407295,-!p1@Ikzf3!0.86!6.30!Ikzf3;;chr9:96159210..96159221,+!p10@Tfdp2!0.86!6.30!Tfdp2;;chr6:52176164..52176195,-!p1@Hoxa9!0.85!7.76!Hoxa9;;chr15:103164702..103164778,-!p3@Zfp385a!0.85!7.27!Zfp385a;;chr2:74542918..74542971,+!p1@Hoxd8!0.84!9.21!Hoxd8;;chr6:86619104..86619119,-!p1@Mxd1!0.83!50.43!Mxd1;;chr11:120491440..120491474,-!p3@Mafg!0.83!8.73!Mafg;;chr15:103085802..103085817,-!p4@Nfe2!0.83!7.27!Nfe2;;chr13:83643232..83643254,+!p5@Mef2c!0.83!5.82!Mef2c;;chr16:25684232..25684285,+!p2@Trp63!0.83!5.82!Trp63;;chr2:91864300..91864379,-!p2@Creb3l1!0.82!16.97!Creb3l1;;chr5:24108047..24108106,-!p3@Smarcd3!0.82!10.18!Smarcd3;;chr8:124806048..124806094,+!p1@Zfpm1!0.81!54.31!Zfpm1;;chr10:20880629..20880683,-!p1@Myb!0.80!16.49!Myb;;chr11:100683794..100683805,-!p4@Stat5b!0.80!5.33!Stat5b;;chr5:104183477..104183548,+!p6@Aff1!0.79!10.67!Aff1;;chr16:43363152..43363186,+!p3@Zbtb20!0.78!12.12!Zbtb20;;chr8:87225702..87225726,+!p3@Lyl1!0.78!10.67!Lyl1;;chr5:65203599..65203617,+!p8@Klf3!0.78!8.73!Klf3;;chr4:63064364..63064384,-!p1@Akna!0.77!15.52!Akna;;chr4:135728473..135728494,+!p5@E2f2!0.77!4.85!E2f2;;chr3:99057256..99057268,+!p3@Tbx15!0.77!4.85!Tbx15;;chr15:102797225..102797243,+!p2@Hoxc10!0.77!4.85!Hoxc10;;chr7:56136362..56136400,-!p1@E2f8!0.76!33.94!E2f8;;chr2:90936901..90936945,+!p1@Sfpi1!0.76!27.64!Sfpi1;;chr5:135582751..135582788,+!p1@Mlxipl!0.76!20.85!Mlxipl;;chr10:5734525..5734569,-!p3@Esr1!0.76!8.24!Esr1;;chr17:48015645..48015689,-!p9@Foxp4!0.76!6.30!Foxp4;;chr5:65203575..65203589,+!p11@Klf3!0.76!5.82!Klf3;;chr12:37835141..37835194,+!p1@Meox2!0.74!15.03!Meox2;;chr10:5636374..5636421,-!p1@Esr1!0.74!5.82!Esr1;;chr2:90936978..90937023,+!p3@Sfpi1!0.73!8.73!Sfpi1;;chr7:25917492..25917512,-!p1@Pou2f2!0.73!7.76!Pou2f2;;chr9:63514630..63514652,-!p8@Smad3!0.73!4.36!Smad3;;chr3:66785201..66785226,-!p3@Shox2!0.73!4.36!Shox2;;chr1:167865149..167865167,-!p3@Pou2f1!0.73!4.36!Pou2f1;;chr7:122989676..122989687,-!p8@Sox6!0.73!4.36!Sox6;;chr13:83663902..83663927,+!p1@Mef2c!0.72!116.85!Mef2c;;chr2:65683890..65683907,+!p1@Csrnp3!0.72!8.73!Csrnp3;;chr13:112476264..112476282,+!p3@Mier3!0.72!6.30!Mier3;;chr11:44430788..44430804,+!p3@Ebf1!0.71!11.15!Ebf1;;chr17:44872561..44872615,-!p1@Runx2!0.71!10.18!Runx2;;chr2:90936947..90936977,+!p2@Sfpi1!0.71!8.73!Sfpi1;;chr16:92697560..92697592,-!p2@Runx1!0.69!27.64!Runx1;;chr8:87225329..87225396,+!p1@Lyl1!0.69!16.49!Lyl1;;chr5:24107993..24108036,-!p2@Smarcd3!0.69!10.18!Smarcd3;;chr15:50720601..50720630,-!p2@Trps1!0.69!10.18!Trps1;;chr9:96159427..96159432,+!p11@Tfdp2!0.69!4.85!Tfdp2;;chr15:103083199..103083215,-!p8@Nfe2!0.69!3.88!Nfe2;;chr15:102797288..102797302,+!p1@Hoxc10!0.69!3.88!Hoxc10;;chr11:96880072..96880079,+!p1@Sp6!0.69!3.88!Sp6;;chr1:57028157..57028173,-!p3@Satb2!0.69!3.88!Satb2;;chr1:38721767..38721778,-!p5@Aff3!0.69!3.88!Aff3;;chr4:44723835..44723849,-!p4@Pax5!0.69!3.88!Pax5;;chr4:44717334..44717367,-!p5@Pax5!0.69!3.88!Pax5;;chr14:79915425..79915501,+!p1@Elf1!0.68!38.79!Elf1;;chr4:32325688..32325777,+!p1@Bach2!0.68!37.82!Bach2;;chr7:87170879..87170914,+!p2@Zfp710!0.68!9.70!Zfp710;;chr11:11585678..11585745,+!p5@Ikzf1!0.68!5.82!Ikzf1;;chr2:90922554..90922575,+!p4@Sfpi1!0.67!7.27!Sfpi1;;chr7:123177377..123177409,-!p7@Sox6!0.67!4.85!Sox6;;chr11:96690797..96690813,-!p1@Nfe2l1!0.66!79.52!Nfe2l1;;chr15:102087737..102087801,-!p3@Rarg!0.66!6.30!Rarg;;chr16:92697354..92697362,-!p3@Runx1!0.66!5.82!Runx1;;chr8:123260252..123260264,+!p1@Irf8!0.65!28.12!Irf8;;chr11:101755669..101755686,-!p1@Meox1!0.65!6.79!Meox1;;chr10:5636354..5636373,-!p2@Esr1!0.64!3.39!Esr1;;chr10:106931803..106931817,-!p2@Myf6!0.64!3.39!Myf6;;chr15:102828658..102828678,+!p1@Hoxc6!0.64!3.39!Hoxc6;;chr14:55330976..55330990,-!p1@Cebpe!0.64!3.39!Cebpe;;chr6:52184901..52184959,-!p2@Hoxa10!0.64!3.39!Hoxa10;;chr2:166868994..166869023,-!p7@Znfx1!0.64!3.39!Znfx1;;chr1:136186574..136186592,+!p1@Myog!0.64!3.39!Myog;;chr2:91864661..91864686,-!p1@Creb3l1!0.62!82.91!Creb3l1;;chr12:86940338..86940357,+!p1@Jdp2!0.62!37.34!Jdp2;;chr2:162880327..162880385,+!p2@Mybl2!0.62!24.73!Mybl2;;chr5:104121453..104121479,+!p4@Aff1!0.62!16.97!Aff1;;chr3:130813200..130813252,+!p1@Lef1!0.62!16.49!Lef1;;chr16:23988686..23988693,-!p2@Bcl6!0.62!7.27!Bcl6;;chr6:29476690..29476724,+!p1@Irf5!0.61!16.97!Irf5;;chr6:145814003..145814056,-!p1@Bhlhe41!0.61!10.18!Bhlhe41;;chr13:55932591..55932622,-!p1@Pitx1!0.61!3.88!Pitx1;;chr13:83663868..83663894,+!p2@Mef2c!0.60!51.40!Mef2c;;chr4:134708451..134708469,+!p1@Runx3!0.60!5.82!Runx3;;chr11:101413151..101413207,-!p1@Brca1!0.59!33.94!Brca1;;chr9:48644037..48644067,-!p2@Zbtb16!0.59!8.24!Zbtb16;;chr1:165243591..165243625,-!p2@Prrx1!0.59!4.85!Prrx1;;chr7:52963269..52963305,+!p4@Dbp!0.59!4.36!Dbp;;chr1:38721779..38721790,-!p6@Aff3!0.59!2.91!Aff3;;chr1:122498955..122498968,+!p1@En1!0.59!2.91!En1;;chr4:114729957..114730012,+!p3@Tal1!0.59!2.91!Tal1;;chr4:114732159..114732166,+!p6@Tal1!0.59!2.91!Tal1;;chr3:66785857..66785873,-!p1@Shox2!0.59!2.91!Shox2;;chr4:87452167..87452178,-!p8@Mllt3!0.59!2.91!Mllt3;;chr11:85699862..85699920,+!p1@Tbx4!0.59!2.91!Tbx4;;chr15:75578748..75578752,-!p1@Mafa!0.59!2.91!Mafa;;chr6:144152648..144152680,-!p5@Sox5!0.59!2.91!Sox5;;chr6:115372058..115372085,+!p3@Pparg!0.59!2.91!Pparg;;chr6:6812962..6812979,+!p1@Dlx6!0.59!2.91!Dlx6;;chr17:44951598..44951609,-!p12@Runx2!0.59!2.91!Runx2;;chr2:160192793..160192809,-!p1@Mafb!0.58!51.88!Mafb;;chr14:47896467..47896523,-!p1@Wdhd1!0.58!41.70!Wdhd1;;chr5:20387850..20387869,-!p1@Phtf2!0.58!34.91!Phtf2;;chr19:53384910..53384937,+!p3@Mxi1!0.58!9.21!Mxi1;;chr11:96690779..96690790,-!p3@Nfe2l1!0.58!7.76!Nfe2l1;;chr11:23670953..23671028,-!p1@Rel!0.55!17.94!Rel;;chr9:48644306..48644364,-!p1@Zbtb16!0.55!12.61!Zbtb16;;chr11:44431016..44431045,+!p5@Ebf1!0.55!3.88!Ebf1;;chr5:24107903..24107917,-!p6@Smarcd3!0.55!3.39!Smarcd3;;chr15:75578637..75578669,-!p2@Mafa!0.55!2.91!Mafa;;chr5:104183219..104183236,+!p2@Aff1!0.54!21.33!Aff1;;chr4:133276698..133276743,-!p6@Arid1a!0.54!8.24!Arid1a;;chr10:41995430..41995458,-!p3@Foxo3!0.54!7.76!Foxo3;;chr11:5761979..5761992,+!p2@Aebp1!0.54!5.82!Aebp1;;chr11:44430877..44430899,+!p6@Ebf1!0.54!3.39!Ebf1;;chr4:114730254..114730276,+!p2@Tal1!0.54!3.39!Tal1;;chr17:56970339..56970428,-!p1@Rfx2!0.53!9.21!Rfx2;;chr2:56976543..56976558,-!p2@Nr4a2!0.53!6.30!Nr4a2;;chr7:56137011..56137041,-!p2@E2f8!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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011467
 |is_obsolete=
+|library_id=CNhs11195
+|library_id_phase_based=2:CNhs11195
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1350
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1350
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm9.nobarcode.rdna.fa.gz
 |name=bone (os femoris), neonate N20
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11195,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.802858127525329,0,0,0,0,0.383934373725717,0,0,0,0,0,0,0.102517869892262,0,0,0,0,0,0,0,0,0,0,0,0,0,0.033670821244,0,0.171689969376673,0,0,0,0.172019691952721,-0.0501889548412364,0.166745710006903,0.314862835492619,-0.0981786686336785,0,0,0,0,0,0,0,0,0,0,0,0,0.105684421813232,0,0,0,0,-0.0428469550828748,0,0.16371465532405,1.48192945358188,1.80310808984322,0.00470661936509711,0.0399228775187438,0.281442956228645,0.0135989266055902,0.0291989313178313,0,0.1190727759113,-0.00899272883521196,-0.202676690736533,0.389985287491827,0.0858449846883365,0,-0.0267550188853343,0.17114836542326,0.31115369265192,0,0,0,0,0,0,0.161624332336363,0.338006298903541,0.111539415217148,0.0971357144691687,0,0,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=IRF7:5.09789043893;MEF2{A,B,C,D}:2.18671776533;GLI1..3:2.18258711915;FOXL1:2.09566439793;GATA6:1.95586490177;NR3C1:1.85831057367;TAL1_TCF{3,4,12}:1.83084686559;HOX{A5,B5}:1.73986798143;ESR1:1.7147320894;TLX2:1.69930133243;NFE2L2:1.63665088023;NR6A1:1.6047720031;TOPORS:1.58588550292;POU1F1:1.51825669438;NKX2-3_NKX2-5:1.44830404161;IKZF2:1.22159098491;ALX1:1.13844084994;AIRE:1.1216954468;EVI1:1.11715699194;GFI1:1.05078444878;UFEwm:0.998286883263;PAX2:0.985775578571;NFATC1..3:0.980894386273;POU5F1:0.970780874593;E2F1..5:0.943956522192;RXRA_VDR{dimer}:0.937945661255;HES1:0.93527699065;SPIB:0.911311870274;DMAP1_NCOR{1,2}_SMARC:0.893692562732;TGIF1:0.843045547642;NR1H4:0.841496040674;MAFB:0.834328719176;TFAP4:0.830353274914;HMGA1,2:0.825132453012;ZNF238:0.811131715407;FOXO1,3,4:0.801844954736;RUNX1..3:0.785522367108;SRF:0.773043601454;PPARG:0.761610918043;SPI1:0.752950913085;STAT2,4,6:0.723382831134;TEF:0.719192672317;FOXP1:0.714886450475;ARID5B:0.681093187125;FOXP3:0.678750060121;GATA4:0.659266412524;NFE2:0.643026333329;PAX1,9:0.637467195379;EBF1:0.601932968115;HOX{A4,D4}:0.55833746261;PBX1:0.526380870863;PAX4:0.512784368045;MTF1:0.51033570194;PRDM1:0.442075782081;ZNF384:0.439912435347;KLF4:0.437224374476;ALX4:0.426958033001;TEAD1:0.419281215576;ETS1,2:0.408021763878;NR5A1,2:0.3558867429;TBP:0.315237537153;IRF1,2:0.303773592017;SOX5:0.290090483796;ZNF423:0.268902127511;ELF1,2,4:0.221325286043;FOX{F1,F2,J1}:0.214257479894;ZBTB16:0.21234072331;TFAP2{A,C}:0.206899133097;NFKB1_REL_RELA:0.164425342108;ATF6:0.15648286453;MYBL2:0.152132944483;MYB:0.134998577919;RXR{A,B,G}:0.1227180004;POU2F1..3:0.0919486239566;CDX1,2,4:0.0830435445745;PDX1:0.0665026558345;MYFfamily:0.0652420453423;HOXA9_MEIS1:0.0572840215252;TLX1..3_NFIC{dimer}:0.0538052951692;YY1:0.0429717960356;PITX1..3:-0.00231924418759;STAT5{A,B}:-0.013198237065;GTF2A1,2:-0.0229039489951;ZNF148:-0.0231443922045;SPZ1:-0.026423897652;MAZ:-0.0275173898076;RREB1:-0.0286523367289;CDC5L:-0.0349395342936;NHLH1,2:-0.050150484901;NANOG{mouse}:-0.0577207329868;GCM1,2:-0.0625631038719;SOX{8,9,10}:-0.066787114497;HSF1,2:-0.0673762126804;NKX2-2,8:-0.0797563280596;EP300:-0.0942582542863;CEBPA,B_DDIT3:-0.0951603335854;PAX8:-0.13028910818;TBX4,5:-0.136342348743;FOS_FOS{B,L1}_JUN{B,D}:-0.14630584755;MZF1:-0.148592077714;MTE{core}:-0.157788001728;MYOD1:-0.159231492275;TFCP2:-0.165110924064;LMO2:-0.182831975293;BACH2:-0.200547536615;FOX{I1,J2}:-0.227376566552;SREBF1,2:-0.229229093069;HIF1A:-0.231018245608;FOXA2:-0.247288369684;GFI1B:-0.277311287535;ESRRA:-0.280470197728;LHX3,4:-0.282108115278;ZIC1..3:-0.285589431267;NFY{A,B,C}:-0.296209951708;PAX6:-0.297298187216;GTF2I:-0.300589087294;PATZ1:-0.34051086761;RFX2..5_RFXANK_RFXAP:-0.356407322581;SMAD1..7,9:-0.38240756163;IKZF1:-0.384511472356;NKX6-1,2:-0.403503014483;HIC1:-0.410987927047;HLF:-0.418259378553;POU6F1:-0.419888242286;FOSL2:-0.428187077628;BPTF:-0.437618438755;NKX2-1,4:-0.469846451323;CRX:-0.475873109831;TFDP1:-0.478887168168;TFAP2B:-0.489361351036;XCPE1{core}:-0.496856960235;ZNF143:-0.512825778941;NFE2L1:-0.538018830077;TP53:-0.566613170721;ATF5_CREB3:-0.579720262212;MED-1{core}:-0.618933941324;HBP1_HMGB_SSRP1_UBTF:-0.632825862064;SP1:-0.634445488311;BREu{core}:-0.645277125327;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.665950410251;CREB1:-0.67359076361;HNF4A_NR2F1,2:-0.680277399402;POU3F1..4:-0.758328239733;EGR1..3:-0.765253964884;PAX5:-0.77475366968;SOX17:-0.785111314395;ZFP161:-0.792163842195;AR:-0.834447647559;NRF1:-0.857272918865;RFX1:-0.872377134582;HNF1A:-0.883163336661;PRRX1,2:-0.884005053373;JUN:-0.889888716125;T:-0.900058314889;CUX2:-0.908544297436;ZBTB6:-0.92199807501;REST:-0.952440143887;FOX{D1,D2}:-0.964264329044;ATF4:-0.979141708525;EN1,2:-0.996108144587;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.00817630287;ATF2:-1.0108745712;FOXM1:-1.02953981711;AHR_ARNT_ARNT2:-1.05713990965;RORA:-1.05958358629;NKX3-2:-1.07727761305;HMX1:-1.1494694208;OCT4_SOX2{dimer}:-1.16735039136;DBP:-1.16846961762;ELK1,4_GABP{A,B1}:-1.18246261667;NFIL3:-1.21405881593;SNAI1..3:-1.2515986516;VSX1,2:-1.27722567057;SOX2:-1.28836369768;RBPJ:-1.32468189218;ZEB1:-1.4042090536;NFIX:-1.42797354857;bHLH_family:-1.43495777006;NKX3-1:-1.47026232696;HAND1,2:-1.53319287202;FOXN1:-1.67414159187;LEF1_TCF7_TCF7L1,2:-1.69410064223;NANOG:-1.72412547557;GZF1:-1.79754105449;FOXD3:-1.9484642627;ADNP_IRX_SIX_ZHX:-2.16255291388;ONECUT1,2:-2.25823762511;STAT1,3:-2.42170590302;FOXQ1:-3.08110581819
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1350-25C3;search_select_hide=table117:1350-25C3
 }}

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From FANTOM5_SSTAR

Latest revision as of 19:00, 4 June 2020

CNhs11195

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