FF:1531-43D7: Difference between revisions

Latest revision as of 19:08, 4 June 2020

Name:	pancreas, neonate N01
Species:	Mouse (Mus musculus)
Library ID:	CNhs11138
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pancreas
dev stage	1 day 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		SAMD00005262

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11138		CAGE		DRX009061		DRR009935

Accession ID Mm9

Library id		BAM		CTSS
CNhs11138		DRZ001360		DRZ002743

Accession ID Mm10

Library id		BAM		CTSS
CNhs11138		DRZ012710		DRZ014093

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

CNhs11138

0	0
1	0
10	0
100	0
1000	0
1001	0.0187
1002	-0.00154
1003	3.496738e-4
1004	0
1005	0
1006	-0.00402
1007	0.0926
1008	0
1009	0.12
101	0.0501
1010	0.39
1011	5.634715e-4
1012	0
1013	0.306
1014	0.39
1015	0.0957
1016	-0.0484
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.331
1023	0
1024	0.137
1025	0.135
1026	0.135
1027	0
1028	0
1029	-0.013
103	0.242
1030	0
1031	0.241
1032	0.0679
1033	0.0561
1034	0.39
1035	0.135
1036	0.113
1037	0
1038	0.0265
1039	0.0218
104	0
1040	0.0217
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

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: CNhs11138

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0181
MA0003.1	MA0003.1	0.384
MA0004.1	MA0004.1	0.516
MA0006.1	MA0006.1	0.039
MA0007.1	MA0007.1	0.522
MA0009.1	MA0009.1	0.291
MA0014.1	MA0014.1	0.812
MA0017.1	MA0017.1	0.604
MA0018.2	MA0018.2	2.7005e-6
MA0019.1	MA0019.1	0.537
MA0024.1	MA0024.1	7.79718e-4
MA0025.1	MA0025.1	0.48
MA0027.1	MA0027.1	0.594
MA0028.1	MA0028.1	0.478
MA0029.1	MA0029.1	0.924
MA0030.1	MA0030.1	0.917
MA0031.1	MA0031.1	0.779
MA0035.2	MA0035.2	0.753
MA0038.1	MA0038.1	0.916
MA0039.2	MA0039.2	0.0814
MA0040.1	MA0040.1	0.635
MA0041.1	MA0041.1	0.397
MA0042.1	MA0042.1	0.659
MA0043.1	MA0043.1	0.0291
MA0046.1	MA0046.1	2.71062e-16
MA0047.2	MA0047.2	0.00664
MA0048.1	MA0048.1	0.307
MA0050.1	MA0050.1	0.352
MA0051.1	MA0051.1	0.818
MA0052.1	MA0052.1	8.45454e-8
MA0055.1	MA0055.1	0.424
MA0057.1	MA0057.1	0.76
MA0058.1	MA0058.1	0.722
MA0059.1	MA0059.1	0.0217
MA0060.1	MA0060.1	0.889
MA0061.1	MA0061.1	0.989
MA0062.2	MA0062.2	0.176
MA0065.2	MA0065.2	0.405
MA0066.1	MA0066.1	0.495
MA0067.1	MA0067.1	0.0327
MA0068.1	MA0068.1	0.0784
MA0069.1	MA0069.1	0.503
MA0070.1	MA0070.1	0.837
MA0071.1	MA0071.1	0.741
MA0072.1	MA0072.1	0.887
MA0073.1	MA0073.1	0.849
MA0074.1	MA0074.1	0.0374
MA0076.1	MA0076.1	0.119
MA0077.1	MA0077.1	0.846
MA0078.1	MA0078.1	0.706
MA0079.2	MA0079.2	0.53
MA0080.2	MA0080.2	0.135
MA0081.1	MA0081.1	0.403
MA0083.1	MA0083.1	0.0283
MA0084.1	MA0084.1	0.289
MA0087.1	MA0087.1	0.53
MA0088.1	MA0088.1	0.338
MA0090.1	MA0090.1	0.153
MA0091.1	MA0091.1	2.86777e-4
MA0092.1	MA0092.1	0.35
MA0093.1	MA0093.1	0.596
MA0099.2	MA0099.2	0.00182
MA0100.1	MA0100.1	0.0063
MA0101.1	MA0101.1	0.936
MA0102.2	MA0102.2	0.0321
MA0103.1	MA0103.1	5.07519e-5
MA0104.2	MA0104.2	0.898
MA0105.1	MA0105.1	0.705
MA0106.1	MA0106.1	0.309
MA0107.1	MA0107.1	0.64
MA0108.2	MA0108.2	0.014
MA0111.1	MA0111.1	0.75
MA0112.2	MA0112.2	0.0623
MA0113.1	MA0113.1	0.572
MA0114.1	MA0114.1	0.153
MA0115.1	MA0115.1	0.531
MA0116.1	MA0116.1	0.535
MA0117.1	MA0117.1	0.121
MA0119.1	MA0119.1	0.401
MA0122.1	MA0122.1	0.439
MA0124.1	MA0124.1	0.651
MA0125.1	MA0125.1	0.104
MA0131.1	MA0131.1	0.367
MA0135.1	MA0135.1	0.999
MA0136.1	MA0136.1	0.0105
MA0137.2	MA0137.2	0.0522
MA0138.2	MA0138.2	0.0423
MA0139.1	MA0139.1	0.554
MA0140.1	MA0140.1	0.412
MA0141.1	MA0141.1	0.947
MA0142.1	MA0142.1	0.974
MA0143.1	MA0143.1	0.924
MA0144.1	MA0144.1	0.0536
MA0145.1	MA0145.1	0.127
MA0146.1	MA0146.1	0.563
MA0147.1	MA0147.1	0.292
MA0148.1	MA0148.1	0.00179
MA0149.1	MA0149.1	0.116
MA0150.1	MA0150.1	0.0285
MA0152.1	MA0152.1	0.231
MA0153.1	MA0153.1	3.71077e-7
MA0154.1	MA0154.1	0.0619
MA0155.1	MA0155.1	0.105
MA0156.1	MA0156.1	0.263
MA0157.1	MA0157.1	0.642
MA0159.1	MA0159.1	0.726
MA0160.1	MA0160.1	0.244
MA0162.1	MA0162.1	0.771
MA0163.1	MA0163.1	0.0753
MA0164.1	MA0164.1	0.434
MA0258.1	MA0258.1	0.437
MA0259.1	MA0259.1	0.938

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: CNhs11138

Novel motif	Logo	P-value
1	1	0.563
10	10	0.558
100	100	0.675
101	101	0.395
102	102	0.726
103	103	0.296
104	104	0.781
105	105	0.556
106	106	0.0309
107	107	0.657
108	108	0.385
109	109	0.09
11	11	0.618
110	110	0.118
111	111	0.973
112	112	0.317
113	113	0.0307
114	114	0.104
115	115	0.531
116	116	0.902
117	117	0.475
118	118	0.601
119	119	0.473
12	12	0.048
120	120	0.438
121	121	0.0512
122	122	0.592
123	123	0.597
124	124	0.352
125	125	0.806
126	126	0.0637
127	127	0.522
128	128	0.225
129	129	0.433
13	13	6.38317e-4
130	130	0.191
131	131	0.441
132	132	0.806
133	133	0.148
134	134	0.275
135	135	0.642
136	136	0.0507
137	137	0.124
138	138	0.00661
139	139	0.825
14	14	0.918
140	140	0.0503
141	141	0.233
142	142	0.378
143	143	0.646
144	144	0.304
145	145	0.172
146	146	0.993
147	147	0.216
148	148	0.0255
149	149	0.365
15	15	0.786
150	150	0.375
151	151	0.539
152	152	0.00482
153	153	0.317
154	154	0.672
155	155	0.765
156	156	0.00384
157	157	0.239
158	158	0.829
159	159	0.87
160	160	0.149
161	161	0.399
162	162	0.4
163	163	0.671
164	164	0.361
165	165	0.578
166	166	0.354
167	167	0.702
168	168	0.842
169	169	0.0534
17	17	0.403
18	18	0.142
19	19	0.0195
2	2	0.68
20	20	0.745
21	21	0.544
22	22	0.529
23	23	0.898
24	24	0.133
25	25	0.333
26	26	0.00159
27	27	0.951
28	28	0.161
29	29	0.688
3	3	0.892
30	30	0.718
31	31	0.59
32	32	0.149
33	33	0.47
34	34	0.867
35	35	0.257
36	36	0.535
37	37	0.149
38	38	0.784
39	39	0.0566
4	4	0.356
40	40	0.919
41	41	0.0454
42	42	0.511
43	43	0.513
44	44	0.705
45	45	0.795
46	46	0.42
47	47	0.831
48	48	0.887
49	49	0.619
5	5	0.727
50	50	0.26
51	51	0.908
52	52	0.261
53	53	0.804
54	54	0.589
55	55	0.94
56	56	0.508
57	57	0.918
58	58	0.624
59	59	0.335
6	6	0.995
60	60	0.313
61	61	0.221
62	62	0.61
63	63	0.405
64	64	0.913
65	65	0.348
66	66	0.447
67	67	0.718
68	68	0.754
69	69	0.839
7	7	0.205
70	70	0.908
71	71	0.0623
72	72	0.733
73	73	0.0784
74	74	0.291
75	75	0.741
76	76	0.887
77	77	0.238
78	78	0.24
79	79	0.0462
8	8	0.169
80	80	0.278
81	81	0.54
82	82	0.597
83	83	0.816
84	84	0.0061
85	85	0.835
86	86	0.397
87	87	0.28
88	88	0.364
89	89	0.746
9	9	0.67
90	90	0.706
91	91	0.211
92	92	0.592
93	93	0.296
94	94	0.26
95	95	0.889
96	96	0.308
97	97	0.0574
98	98	0.727
99	99	0.261

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: CNhs11138

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011251 mouse pancreas- neonate N01 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)
0001264 (pancreas)
0002100 (trunk)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011251 (mouse pancreas- neonate N01 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
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001045,UBERON:0001048,UBERON:0001062,UBERON:0001264,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002108,UBERON:0002114,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003921,UBERON:0003922,UBERON:0003923,UBERON:0003924,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
+|DRA_sample_Accession=CAGE@SAMD00005262
+|accession_numbers=CAGE;DRX009061;DRR009935;DRZ001360;DRZ002743;DRZ012710;DRZ014093
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001264,UBERON:0002100,UBERON:0000479,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002323,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0000949
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000304,FF:0011251
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:164228702..164228719,+!p1@Rbpjl!2.75!563.48!Rbpjl;;chr2:19367259..19367278,+!p1@Ptf1a!1.99!95.97!Ptf1a;;chr5:144951153..144951203,+!p1@Bhlha15!1.87!103.61!Bhlha15;;chr9:74709695..74709722,+!p1@Onecut1!1.83!66.53!Onecut1;;chr1:138857076..138857105,-!p1@Nr5a2!1.53!32.72!Nr5a2;;chr2:103143336..103143367,-!p1@Ehf!1.47!45.81!Ehf;;chr7:19608891..19608895,-!p1@Foxa3!1.45!35.26!Foxa3;;chr2:79296783..79296801,-!p1@Neurod1!1.42!25.08!Neurod1;;chr11:83664365..83664383,+!p1@Hnf1b!1.30!18.90!Hnf1b;;chr7:6649134..6649167,-!p1@Zim1!1.29!97.06!Zim1;;chr5:148081686..148081715,+!p1@Pdx1!1.26!17.09!Pdx1;;chr11:5420655..5420659,+!p3@Xbp1!1.25!16.72!Xbp1;;chr2:147871627..147871641,-!p1@Foxa2!1.24!16.36!Foxa2;;chr2:163332558..163332596,+!p2@Hnf4a!1.22!15.63!Hnf4a;;chr17:27865882..27865901,-!p1@Spdef!1.20!14.90!Spdef;;chr8:59799772..59799789,+!p1@Hand2!1.18!40.35!Hand2;;chr14:63864056..63864102,-!p1@Gata4!1.15!22.90!Gata4;;chr1:138857048..138857071,-!p2@Nr5a2!1.15!13.09!Nr5a2;;chr1:138857112..138857130,-!p7@Nr5a2!1.06!10.54!Nr5a2;;chr4:133109285..133109308,+!p1@Nr0b2!1.06!10.54!Nr0b2;;chr5:148081722..148081744,+!p2@Pdx1!1.05!10.18!Pdx1;;chr5:104121453..104121479,+!p4@Aff1!1.02!43.62!Aff1;;chr13:117099847..117099907,-!p1@Isl1!1.01!17.09!Isl1;;chr10:88969376..88969395,-!p1@Nr1h4!1.00!9.09!Nr1h4;;chr5:135582751..135582788,+!p1@Mlxipl!0.97!34.17!Mlxipl;;chr14:63890491..63890516,-!p2@Gata4!0.95!8.00!Gata4;;chr1:138846009..138846038,-!p3@Nr5a2!0.91!8.00!Nr5a2;;chr14:63890519..63890539,-!p3@Gata4!0.90!6.91!Gata4;;chr8:90328310..90328362,-!p3@Zfp423!0.88!7.63!Zfp423;;chr19:43686789..43686811,+!p1@Nkx2-3!0.88!6.54!Nkx2-3;;chr11:121380594..121380609,-!p2@Zfp750!0.86!11.27!Zfp750;;chr10:51397572..51397595,+!p1@Rfx6!0.86!6.18!Rfx6;;chr13:48758276..48758291,+!p1@Barx1!0.86!6.18!Barx1;;chr2:147012125..147012149,-!p1@Nkx2-2!0.86!6.18!Nkx2-2;;chr11:5420954..5420969,+!p2@Xbp1!0.85!79.98!Xbp1;;chr4:154010918..154010931,-!p1@Prdm16!0.85!18.90!Prdm16;;chr15:35225845..35225867,+!p1@Osr2!0.84!15.63!Osr2;;chr11:121380640..121380655,-!p1@Zfp750!0.84!10.18!Zfp750;;chr10:61595830..61595846,+!p1@Neurog3!0.83!5.82!Neurog3;;chr3:30039329..30039355,-!p5@Mecom!0.83!5.82!Mecom;;chr2:103264213..103264233,+!p1@Elf5!0.83!5.82!Elf5;;chr2:103143315..103143328,-!p2@Ehf!0.83!5.82!Ehf;;chr10:12810631..12810649,+!p1@Plagl1!0.81!154.87!Plagl1;;chr19:37509324..37509337,+!p1@Hhex!0.81!41.81!Hhex;;chr9:96620459..96620478,-!p9@Zbtb38!0.81!6.18!Zbtb38;;chr9:74714303..74714318,+!p2@Onecut1!0.81!5.45!Onecut1;;chr14:63890545..63890560,-!p5@Gata4!0.81!5.45!Gata4;;chr6:30908793..30908815,-!p1@Klf14!0.81!5.45!Klf14;;chr10:22539932..22539956,-!p1@Tcf21!0.80!14.90!Tcf21;;chr3:30408384..30408431,-!p4@Mecom!0.80!6.91!Mecom;;chr5:125538737..125538781,-!p2@Ncor2!0.78!19.27!Ncor2;;chr5:148081667..148081678,+!p3@Pdx1!0.78!5.09!Pdx1;;chr5:102094214..102094230,-!p1@Nkx6-1!0.78!5.09!Nkx6-1;;chr2:104966766..104966786,+!p1@Wt1!0.77!8.00!Wt1;;chr9:74714281..74714296,+!p5@Onecut1!0.76!4.73!Onecut1;;chr7:148513409..148513455,-!p2@Deaf1!0.73!22.54!Deaf1;;chr14:63890459..63890484,-!p4@Gata4!0.73!4.36!Gata4;;chr1:138846079..138846103,-!p6@Nr5a2!0.73!4.36!Nr5a2;;chr4:154010409..154010466,-!p2@Prdm16!0.71!10.54!Prdm16;;chr15:37162796..37162828,+!p1@Grhl2!0.71!7.27!Grhl2;;chr19:10315179..10315241,-!p1@Gm98!0.70!47.99!Gm98;;chr3:94176733..94176794,+!p1@Rorc!0.70!34.90!Rorc;;chr2:105509045..105509071,+!p1@Pax6!0.70!4.00!Pax6;;chr2:146047829..146047847,+!p1@Insm1!0.68!7.27!Insm1;;chr7:86956107..86956152,+!p@chr7:86956107..86956152,+!0.68!6.18!Mesp2;;chr7:52471143..52471186,+!p1@Tead2!0.67!44.71!Tead2;;chr1:191994550..191994623,-!p1@Prox1!0.67!29.45!Prox1;;chr3:30408603..30408668,-!p1@Mecom!0.67!9.45!Mecom;;chr7:52472041..52472065,+!p2@Tead2!0.67!4.36!Tead2;;chr13:48758358..48758415,+!p2@Barx1!0.67!3.64!Barx1;;chr14:63890691..63890718,-!p8@Gata4!0.67!3.64!Gata4;;chr19:28754692..28754757,-!p1@Glis3!0.66!16.72!Glis3;;chr6:146744595..146744613,+!p2@Arntl2!0.65!6.18!Arntl2;;chr1:138845748..138845766,-!p4@Nr5a2!0.65!4.73!Nr5a2;;chr2:115888250..115888298,-!p10@Meis2!0.65!4.36!Meis2;;chr10:114821444..114821491,-!p1@Thap2!0.63!30.90!Thap2;;chr5:138187583..138187602,+!p6@Tsc22d4!0.63!6.54!Tsc22d4;;chr1:6720216..6720232,+!p1@St18!0.63!3.27!St18;;chr9:74709682..74709691,+!p3@Onecut1!0.63!3.27!Onecut1;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!0.63!3.27!Ppard;;chr7:6683123..6683142,-!p1@Peg3!0.62!195.58!Peg3;;chr11:44431687..44431706,+!p2@Ebf1!0.62!17.45!Ebf1;;chr12:37835141..37835194,+!p1@Meox2!0.62!11.27!Meox2;;chr2:115890469..115890485,-!p7@Meis2!0.62!5.45!Meis2;;chr1:69732511..69732540,-!p2@Ikzf2!0.62!4.36!Ikzf2;;chr2:91864661..91864686,-!p1@Creb3l1!0.61!80.34!Creb3l1;;chr2:168415815..168415872,-!p1@Nfatc2!0.61!19.63!Nfatc2;;chr10:88996336..88996380,-!p2@Nr1h4!0.61!4.00!Nr1h4;;chr18:80904854..80904919,-!p2@Nfatc1!0.60!42.53!Nfatc1;;chrX:45245679..45245702,-!p1@Smarca1!0.60!15.63!Smarca1;;chr6:51382677..51382783,+!p1@Nfe2l3!0.60!8.72!Nfe2l3;;chr10:126778916..126778974,-!p1@Gli1!0.60!7.63!Gli1;;chr14:22807083..22807104,-!p1@Zfp503!0.59!62.16!Zfp503;;chr8:124806048..124806094,+!p1@Zfpm1!0.59!31.99!Zfpm1;;chr1:194979315..194979359,+!p1@Irf6!0.59!21.45!Irf6;;chr11:18918820..18918831,-!p4@Meis1!0.59!6.18!Meis1;;chr2:147012101..147012118,-!p3@Nkx2-2!0.59!2.91!Nkx2-2;;chr2:147019977..147019985,-!p2@Nkx2-2!0.59!2.91!Nkx2-2;;chr19:55972767..55972779,+!p20@Tcf7l2!0.59!2.91!Tcf7l2;;chr14:63890660..63890687,-!p7@Gata4!0.59!2.91!Gata4;;chr17:14011485..14011507,+!p2@Mllt4!0.59!2.91!Mllt4;;chr3:29911808..29911833,-!p8@Mecom!0.59!2.91!Mecom;;chr18:11052485..11052508,+!p2@Gata6!0.58!9.09!Gata6;;chr11:98605517..98605539,+!p5@Thra!0.58!4.36!Thra;;chr2:91864300..91864379,-!p2@Creb3l1!0.57!9.09!Creb3l1;;chr6:52154414..52154462,-!p1@Hoxa5!0.57!4.00!Hoxa5;;chr4:97444537..97444555,+!p8@Nfia!0.56!7.63!Nfia;;chr1:135557526..135557551,-!p1@Zbed6!0.56!4.73!Zbed6;;chr11:5420973..5420992,+!p1@Xbp1!0.55!338.81!Xbp1;;chr11:112643496..112643562,+!p1@Sox9!0.55!119.97!Sox9;;chr1:165243792..165243808,-!p1@Prrx1!0.55!10.91!Prrx1;;chr3:3508024..3508069,+!p2@Hnf4g!0.55!2.54!Hnf4g;;chr13:56804865..56804898,+!p3@Smad5!0.54!7.63!Smad5;;chr19:28754600..28754612,-!p2@Glis3!0.54!4.36!Glis3;;chr12:9581262..9581282,+!p1@Osr1!0.53!36.35!Osr1;;chr5:134790276..134790294,-!p7@Gtf2i!0.53!6.18!Gtf2i;;chr2:91864449..91864492,-!p3@Creb3l1!0.53!4.36!Creb3l1;;chr2:115890953..115890974,-!p6@Meis2!0.53!4.00!Meis2;;chr7:17642053..17642066,-!p2@Hif3a!0.53!3.64!Hif3a;;chr16:22439681..22439698,-!p1@Etv5!0.52!52.71!Etv5;;chr18:11052642..11052659,+!p1@Gata6!0.52!14.54!Gata6;;chr16:22439654..22439676,-!p2@Etv5!0.51!17.09!Etv5;;chr6:72849280..72849297,-!p6@Kcmf1!0.51!5.09!Kcmf1;;chr8:90483433..90483457,-!p2@Zfp423!0.51!3.27!Zfp423;;chr11:121380611..121380625,-!p3@Zfp750!0.51!2.91!Zfp750;;chr14:64562503..64562524,+!p1@Sox7!0.50!16.36!Sox7;;chr18:11052456..11052477,+!p3@Gata6!0.50!8.36!Gata6;;chr10:114821393..114821431,-!p5@Thap2!0.50!7.27!Thap2;;chr6:52114821..52114828,-!p1@Hoxa2!0.50!3.64!Hoxa2;;chr12:30213247..30213333,+!p1@Myt1l!0.50!2.18!Myt1l;;chr2:147872790..147872821,-!p2@Foxa2!0.50!2.18!Foxa2;;chr11:83664334..83664353,+!p2@Hnf1b!0.50!2.18!Hnf1b;;chr16:43235969..43235989,+!p20@Zbtb20!0.50!2.18!Zbtb20;;chr5:104121391..104121450,+!p3@Aff1!0.49!14.18!Aff1;;chr2:34227446..34227511,-!p1@Pbx3!0.49!5.82!Pbx3;;chr14:67853457..67853482,+!p2@Ebf2!0.49!3.27!Ebf2;;chr6:52154386..52154407,-!p2@Hoxa5!0.49!2.91!Hoxa5;;chr11:85646303..85646329,+!p1@Tbx2!0.48!17.81!Tbx2;;chr15:102865088..102865107,+!p1@Hoxc4!0.48!2.91!Hoxc4;;chr18:69680960..69681007,+!p10@Tcf4!0.48!2.91!Tcf4;;chr9:63605740..63605771,-!p1@Smad3!0.47!38.17!Smad3;;chr4:3865501..3865548,-!p1@Plag1!0.47!13.09!Plag1;;chr6:90412582..90412601,+!p1@Klf15!0.47!12.00!Klf15;;chr16:4594853..4594884,+!p3@Glis2!0.47!3.64!Glis2;;chr14:67853632..67853674,+!p3@Ebf2!0.47!2.54!Ebf2;;chr10:30375579..30375616,-!p3@Ncoa7!0.46!5.45!Ncoa7;;chr3:30408674..30408716,-!p2@Mecom!0.46!3.64!Mecom;;chrX:90531838..90531861,+!p1@Arx!0.46!2.54!Arx;;chr18:69681439..69681456,+!p7@Tcf4!0.45!5.82!Tcf4;;chr18:7004715..7004731,-!p1@Mkx!0.45!5.45!Mkx;;chr16:43236133..43236154,+!p17@Zbtb20!0.45!2.18!Zbtb20;;chr2:79296907..79296918,-!p2@Neurod1!0.45!1.82!Neurod1;;chr2:147871948..147871977,-!p3@Foxa2!0.45!1.82!Foxa2;;chr1:6724908..6724955,+!p2@St18!0.45!1.82!St18;;chr2:104966933..104966966,+!p3@Wt1!0.45!1.82!Wt1;;chr2:105003277..105003280,+!p5@Wt1!0.45!1.82!Wt1;;chr2:147872074..147872079,-!p4@Foxa2!0.45!1.82!Foxa2;;chr9:74709664..74709671,+!p6@Onecut1!0.45!1.82!Onecut1;;chr5:115421065..115421088,-!p1@Hnf1a!0.45!1.82!Hnf1a;;chr5:115420882..115420896,-!p3@Hnf1a!0.45!1.82!Hnf1a;;chr5:42155788..42155800,-!p1@Nkx3-2!0.45!1.82!Nkx3-2;;chr2:115891454..115891471,-!p3@Meis2!0.44!6.91!Meis2;;chr19:26681721..26681746,+!p9@Smarca2!0.44!4.36!Smarca2;;chr2:35960919..35960954,-!p1@Lhx6!0.44!4.00!Lhx6;;chr12:3807076..3807086,+!p8@Dnmt3a!0.44!3.64!Dnmt3a;;chr14:22808697..22808715,-!p4@Zfp503!0.44!2.18!Zfp503;;chr1:93698068..93698085,+!p2@Twist2!0.44!2.18!Twist2;;chr11:106128936..106128955,-!p4@Smarcd2!0.44!2.18!Smarcd2;;chr10:80555320..80555378,-!p1@Creb3l3!0.44!2.18!Creb3l3;;chr14:65977498..65977528,+!p1@Zfp395!0.43!15.63!Zfp395;;chr1:137155026..137155042,-!p1@Elf3!0.43!13.81!Elf3;;chr17:32506357..32506377,-!p3@Wiz!0.43!4.36!Wiz;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.43!2.54!Hoxb2;;chr15:37162834..37162849,+!p2@Grhl2!0.43!2.18!Grhl2;;chr11:18918959..18918976,-!p2@Meis1!0.42!31.99!Meis1;;chr5:147760305..147760324,+!p2@Gtf3a!0.42!10.91!Gtf3a;;chr14:22807107..22807119,-!p2@Zfp503!0.42!9.82!Zfp503;;chr2:169458519..169458555,+!p2@Tshz2!0.42!9.09!Tshz2;;chr9:63605691..63605705,-!p3@Smad3!0.42!5.45!Smad3;;chr1:172797876..172797887,-!p5@Atf6!0.42!4.73!Atf6;;chr6:146744563..146744594,+!p1@Arntl2!0.42!3.64!Arntl2;;chr4:82151500..82151505,-!p11@Nfib!0.42!2.18!Nfib;;chr1:69732682..69732719,-!p4@Ikzf2!0.42!2.18!Ikzf2;;chr1:138846047..138846074,-!p5@Nr5a2!0.42!1.82!Nr5a2;;chr1:172797892..172797915,-!p1@Atf6!0.41!65.07!Atf6;;chr14:7991542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+|ffid_belonging_in_development=FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:1531-43D7
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011251
+|is_a=EFO:0002091;;FF:0011251
+|is_obsolete=
+|library_id=CNhs11138
+|library_id_phase_based=2:CNhs11138
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1531
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1531
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N01.CNhs11138.1531-43D7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N01.CNhs11138.1531-43D7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N01.CNhs11138.1531-43D7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N01.CNhs11138.1531-43D7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N01.CNhs11138.1531-43D7.mm9.nobarcode.rdna.fa.gz
 |name=pancreas, neonate N01
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11138,LSID735,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.109672942865802,0,0,0,0,0.0261039341284844,0.0592441663168585,0,0,0,0,0.614532691279432,0,0,0,0,0,0,-0.0572274654111027,0,0,0,0,0,0,1.2744615815557,0,0,0,0,0,0,0.22615686072732,0,0,0,0,0,-0.01437350813954,0.0156329449803698,-0.0334056208775939,0.643593122702015,0.232722660257661,0,0,0,0.134665885471472,0,0,0,0,0,0,0,0,0.0686603379080315,0,0,0,0,-0.00703881512374357,0,0.0642526519054995,0,0,0.0561061091888273,0.126541332572828,0.355430684146498,0.162180150169807,0.147200674863567,0,0.242262592188938,0.0535585015064517,0.0846766514561962,0,0,0,0.050906555525456,0.188664772310782,0.371058324709766,0,0,0,0,0,0,0.192691130942291,0.401746948935377,0.186324864618363,0,0,0,0,0
 |rna_box=43
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=pancreas
 |top_motifs=RXRA_VDR{dimer}:3.02226229602;EN1,2:2.8272276615;RBPJ:1.9615377456;FOXP1:1.89187260593;TEF:1.59308302806;NR1H4:1.43005842803;ZNF238:1.3860027975;CDX1,2,4:1.34657081939;ARID5B:1.28636978153;SNAI1..3:1.23366573111;FOXA2:1.18481748334;TAL1_TCF{3,4,12}:1.17594707271;GCM1,2:1.15725795969;ONECUT1,2:1.10500707811;MYBL2:1.08306717873;TLX2:1.077389907;ATF6:1.05261073836;IKZF1:1.02133750489;PDX1:0.982765737278;TOPORS:0.980327360611;SPZ1:0.967277131198;STAT5{A,B}:0.93155434189;DBP:0.926046641036;LMO2:0.906361143902;XCPE1{core}:0.894104952195;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.816754618711;MYOD1:0.809350537546;PAX6:0.777260472573;ZNF423:0.775983642207;PAX8:0.759446856313;CEBPA,B_DDIT3:0.738018190869;HNF1A:0.725850267997;ALX4:0.718048497099;ESR1:0.696363177289;STAT1,3:0.678247436983;HAND1,2:0.662699417439;ZEB1:0.655402121268;TFAP4:0.617048198969;PAX1,9:0.580633179231;E2F1..5:0.539311828633;CRX:0.531663749601;TLX1..3_NFIC{dimer}:0.527073844296;AIRE:0.507838388058;FOXD3:0.495844290639;NKX2-2,8:0.486089257987;PITX1..3:0.46773871287;SP1:0.465152004692;bHLH_family:0.456109137989;NFIX:0.448421342851;HMGA1,2:0.446618348964;FOXM1:0.414336256885;HBP1_HMGB_SSRP1_UBTF:0.395429211948;TFAP2B:0.395072529057;GATA6:0.387095636554;GZF1:0.329940179173;NKX3-2:0.304517505576;MTE{core}:0.292949631945;GFI1:0.270015964671;SOX17:0.253293504945;BPTF:0.251001948179;CREB1:0.245968791296;FOX{D1,D2}:0.243354621057;FOX{F1,F2,J1}:0.228789970285;TBP:0.217467486911;PAX4:0.213239574342;ELF1,2,4:0.202047046127;PBX1:0.196691371435;MAZ:0.178823517726;LEF1_TCF7_TCF7L1,2:0.171074735806;TEAD1:0.156132000735;HSF1,2:0.154055922857;EVI1:0.152145948849;CDC5L:0.147359614566;NR6A1:0.144041211102;GTF2I:0.140545308774;ZNF148:0.132822876145;T:0.12966547703;HIC1:0.112010478273;ZBTB16:0.106882778013;PATZ1:0.102490441213;IRF1,2:0.0965266975843;FOXO1,3,4:0.0894659629156;STAT2,4,6:0.0828871413241;UFEwm:0.0826328890535;MTF1:0.0733739978705;NANOG:0.0657484369745;NFY{A,B,C}:0.0653461070427;MED-1{core}:0.0461749610692;TFDP1:0.0397950456702;BREu{core}:0.0198918420233;IKZF2:0.0173367621027;NR5A1,2:0.0159730908695;DMAP1_NCOR{1,2}_SMARC:0.0114501168817;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.00749454162226;ZIC1..3:0.0041716218155;HOX{A5,B5}:0.000437839383896;ALX1:-0.0277290995438;POU6F1:-0.0343786633953;ETS1,2:-0.0536690664154;NR3C1:-0.0594150292007;ADNP_IRX_SIX_ZHX:-0.076818811571;NFIL3:-0.0784390591699;GLI1..3:-0.0821620767898;TFAP2{A,C}:-0.0872373471852;TFCP2:-0.0936729447122;MAFB:-0.107921416488;NRF1:-0.131151655528;PPARG:-0.131847409351;TP53:-0.13715652364;RFX1:-0.138441139875;RXR{A,B,G}:-0.149983479472;SPIB:-0.163838825049;CUX2:-0.167220578025;NKX3-1:-0.172616238765;FOX{I1,J2}:-0.177135221015;ZNF143:-0.181650967957;HNF4A_NR2F1,2:-0.181752507837;ESRRA:-0.189504209704;SOX{8,9,10}:-0.191861151736;EGR1..3:-0.194355609386;SOX2:-0.194462359731;NANOG{mouse}:-0.200817026566;MYFfamily:-0.216273964981;GATA4:-0.230074472663;SMAD1..7,9:-0.250897143317;FOXQ1:-0.259253773666;ELK1,4_GABP{A,B1}:-0.265690742101;HOXA9_MEIS1:-0.281537355717;RREB1:-0.285178705432;HLF:-0.286765630492;EP300:-0.287426073231;NFKB1_REL_RELA:-0.292583193945;PRDM1:-0.296143296097;POU5F1:-0.298269646703;AR:-0.30653245719;ZFP161:-0.310740408648;TGIF1:-0.322978990096;HIF1A:-0.327246706641;SPI1:-0.337399371234;FOXN1:-0.359799963878;SOX5:-0.361768786086;YY1:-0.367479329058;IRF7:-0.368636192357;ATF2:-0.371269859408;GFI1B:-0.379451812349;NFE2L2:-0.382980908061;MYB:-0.383375028423;GTF2A1,2:-0.386643875706;ZNF384:-0.404566606741;SRF:-0.434026479889;NKX2-1,4:-0.44870673734;ZBTB6:-0.459385289304;MZF1:-0.471294540397;PRRX1,2:-0.473470276299;AHR_ARNT_ARNT2:-0.473802730856;FOS_FOS{B,L1}_JUN{B,D}:-0.491613270701;LHX3,4:-0.504269344588;RUNX1..3:-0.509026995495;REST:-0.52257543853;NFATC1..3:-0.537198703251;NHLH1,2:-0.561261600749;POU2F1..3:-0.568862216861;HOX{A4,D4}:-0.571422298296;PAX5:-0.573597248938;HMX1:-0.588536421969;POU1F1:-0.58922285857;BACH2:-0.60496524043;MEF2{A,B,C,D}:-0.662945054582;KLF4:-0.6890875835;FOXL1:-0.690137443028;RFX2..5_RFXANK_RFXAP:-0.726146155749;NFE2:-0.754804791909;ATF5_CREB3:-0.756939657061;OCT4_SOX2{dimer}:-0.757814502105;RORA:-0.758416551266;EBF1:-0.877442435023;NKX2-3_NKX2-5:-0.902084728394;PAX2:-0.910263546805;HES1:-0.911472764386;JUN:-0.914322366043;FOXP3:-1.03519595043;ATF4:-1.03831187743;SREBF1,2:-1.08915624242;NKX6-1,2:-1.09571385878;VSX1,2:-1.16737605282;FOSL2:-1.17031688862;POU3F1..4:-1.40572645434;NFE2L1:-1.83055558312;TBX4,5:-2.30008035748
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1531-43D7;search_select_hide=table117:1531-43D7
 }}

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FF:1531-43D7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:08, 4 June 2020

CNhs11138

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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