Difference between revisions of "FF:59-29C1"

Revision as of 19:07, 27 June 2012

Name:	submandibular gland, adult
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/6J
tissue	submandibular gland
dev stage	adult
sex	male
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

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

CNhs10469

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0
100	0
1000	0
1001	0
1002	--0.0663
1003	0.173
1004	0
1005	0.171
1006	0
1007	--0.0396
1008	0
1009	--0.0572
101	--0.0707
1010	0
1011	0.12
1012	0
1013	0.556
1014	--0.0874
1015	--0.196
1016	--0.255
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.731
1023	0
1024	--0.0899
1025	0
1026	0
1027	--0.048
1028	0
1029	0.027
103	--0.0787
1030	0
1031	--0.417
1032	0.167
1033	--0.0752
1034	0.728
1035	0
1036	--0.233
1037	0.457
1038	--0.0619
1039	0.194
104	0
1040	--0.0865
1041	0.21

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family 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 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 this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon

link to dataset.
data

library id: CNhs10469

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.143
MA0003.1	MA0003.1	0.135
MA0004.1	MA0004.1	0.419
MA0006.1	MA0006.1	0.351
MA0007.1	MA0007.1	0.166
MA0009.1	MA0009.1	0.0675
MA0014.1	MA0014.1	0.195
MA0017.1	MA0017.1	0.891
MA0018.2	MA0018.2	0.0522
MA0019.1	MA0019.1	9.21722e-4
MA0024.1	MA0024.1	4.93387e-5
MA0025.1	MA0025.1	0.489
MA0027.1	MA0027.1	0.211
MA0028.1	MA0028.1	0.57
MA0029.1	MA0029.1	0.36
MA0030.1	MA0030.1	0.598
MA0031.1	MA0031.1	0.765
MA0035.2	MA0035.2	0.0109
MA0038.1	MA0038.1	0.533
MA0039.2	MA0039.2	0.009
MA0040.1	MA0040.1	0.682
MA0041.1	MA0041.1	0.187
MA0042.1	MA0042.1	0.661
MA0043.1	MA0043.1	0.0123
MA0046.1	MA0046.1	9.6203e-8
MA0047.2	MA0047.2	0.326
MA0048.1	MA0048.1	0.541
MA0050.1	MA0050.1	0.00101
MA0051.1	MA0051.1	0.172
MA0052.1	MA0052.1	0.176
MA0055.1	MA0055.1	0.899
MA0057.1	MA0057.1	0.165
MA0058.1	MA0058.1	0.544
MA0059.1	MA0059.1	0.262
MA0060.1	MA0060.1	1.48918e-5
MA0061.1	MA0061.1	0.779
MA0062.2	MA0062.2	0.406
MA0065.2	MA0065.2	0.0582
MA0066.1	MA0066.1	0.973
MA0067.1	MA0067.1	0.19
MA0068.1	MA0068.1	0.263
MA0069.1	MA0069.1	0.854
MA0070.1	MA0070.1	0.686
MA0071.1	MA0071.1	0.574
MA0072.1	MA0072.1	0.346
MA0073.1	MA0073.1	0.559
MA0074.1	MA0074.1	0.743
MA0076.1	MA0076.1	0.434
MA0077.1	MA0077.1	0.507
MA0078.1	MA0078.1	0.438
MA0079.2	MA0079.2	0.224
MA0080.2	MA0080.2	2.55551e-7
MA0081.1	MA0081.1	0.405
MA0083.1	MA0083.1	0.18
MA0084.1	MA0084.1	0.188
MA0087.1	MA0087.1	0.665
MA0088.1	MA0088.1	0.622
MA0090.1	MA0090.1	0.768
MA0091.1	MA0091.1	0.58
MA0092.1	MA0092.1	0.312
MA0093.1	MA0093.1	0.428
MA0099.2	MA0099.2	0.673
MA0100.1	MA0100.1	0.227
MA0101.1	MA0101.1	0.878
MA0102.2	MA0102.2	0.0556
MA0103.1	MA0103.1	1.408e-6
MA0104.2	MA0104.2	0.802
MA0105.1	MA0105.1	0.238
MA0106.1	MA0106.1	0.245
MA0107.1	MA0107.1	0.926
MA0108.2	MA0108.2	0.00492
MA0111.1	MA0111.1	0.717
MA0112.2	MA0112.2	2.33173e-5
MA0113.1	MA0113.1	0.162
MA0114.1	MA0114.1	0.809
MA0115.1	MA0115.1	0.654
MA0116.1	MA0116.1	0.665
MA0117.1	MA0117.1	0.352
MA0119.1	MA0119.1	0.457
MA0122.1	MA0122.1	0.582
MA0124.1	MA0124.1	0.259
MA0125.1	MA0125.1	0.0961
MA0131.1	MA0131.1	0.435
MA0135.1	MA0135.1	0.953
MA0136.1	MA0136.1	3.80647e-5
MA0137.2	MA0137.2	0.717
MA0138.2	MA0138.2	0.292
MA0139.1	MA0139.1	0.694
MA0140.1	MA0140.1	0.145
MA0141.1	MA0141.1	3.27938e-4
MA0142.1	MA0142.1	0.112
MA0143.1	MA0143.1	0.077
MA0144.1	MA0144.1	0.6
MA0145.1	MA0145.1	4.39821e-4
MA0146.1	MA0146.1	0.65
MA0147.1	MA0147.1	0.791
MA0148.1	MA0148.1	0.099
MA0149.1	MA0149.1	0.743
MA0150.1	MA0150.1	0.341
MA0152.1	MA0152.1	0.433
MA0153.1	MA0153.1	8.85292e-6
MA0154.1	MA0154.1	0.0192
MA0155.1	MA0155.1	0.371
MA0156.1	MA0156.1	2.01714e-4
MA0157.1	MA0157.1	0.394
MA0159.1	MA0159.1	0.0196
MA0160.1	MA0160.1	0.0239
MA0162.1	MA0162.1	0.692
MA0163.1	MA0163.1	0.692
MA0164.1	MA0164.1	0.761
MA0258.1	MA0258.1	0.0106
MA0259.1	MA0259.1	0.837

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 in 169 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: CNhs10469

Novel motif	Logo	P-value
1	1	0.11
10	10	0.117
100	100	0.955
101	101	0.176
102	102	0.495
103	103	0.0257
104	104	0.496
105	105	0.31
106	106	0.017
107	107	0.123
108	108	0.946
109	109	0.408
11	11	0.462
110	110	0.393
111	111	0.0234
112	112	0.155
113	113	0.308
114	114	0.358
115	115	0.53
116	116	0.143
117	117	0.461
118	118	0.691
119	119	0.0711
12	12	0.689
120	120	0.693
121	121	0.59
122	122	0.167
123	123	0.242
124	124	0.342
125	125	0.0956
126	126	0.285
127	127	0.087
128	128	0.0597
129	129	0.147
13	13	0.00151
130	130	0.478
131	131	0.525
132	132	0.551
133	133	0.112
134	134	0.504
135	135	0.879
136	136	0.357
137	137	0.864
138	138	0.307
139	139	0.334
14	14	0.544
140	140	0.0729
141	141	0.117
142	142	0.409
143	143	0.276
144	144	0.528
145	145	0.224
146	146	0.579
147	147	0.845
148	148	0.918
149	149	0.813
15	15	0.332
150	150	0.132
151	151	0.126
152	152	0.0862
153	153	0.588
154	154	0.784
155	155	0.292
156	156	1.44495e-12
157	157	0.382
158	158	0.388
159	159	0.143
160	160	0.298
161	161	0.999
162	162	0.334
163	163	0.611
164	164	0.39
165	165	0.633
166	166	0.71
167	167	0.726
168	168	0.171
169	169	0.0508
17	17	0.0806
18	18	0.9
19	19	0.16
2	2	0.673
20	20	0.749
21	21	0.815
22	22	0.377
23	23	0.232
24	24	0.0744
25	25	0.618
26	26	0.0057
27	27	0.522
28	28	0.631
29	29	0.839
3	3	0.497
30	30	0.357
31	31	0.723
32	32	0.724
33	33	0.636
34	34	0.913
35	35	0.479
36	36	0.572
37	37	0.0701
38	38	0.489
39	39	0.445
4	4	0.671
40	40	0.727
41	41	0.529
42	42	0.301
43	43	0.215
44	44	0.835
45	45	0.401
46	46	0.119
47	47	0.335
48	48	0.293
49	49	0.163
5	5	0.186
50	50	0.634
51	51	0.773
52	52	0.198
53	53	0.737
54	54	0.74
55	55	0.319
56	56	0.487
57	57	0.714
58	58	0.137
59	59	0.154
6	6	0.574
60	60	0.136
61	61	0.209
62	62	0.182
63	63	0.0747
64	64	0.972
65	65	0.233
66	66	0.636
67	67	0.735
68	68	0.432
69	69	0.665
7	7	0.144
70	70	0.00698
71	71	0.076
72	72	0.488
73	73	0.0829
74	74	0.945
75	75	0.244
76	76	0.414
77	77	0.371
78	78	0.226
79	79	0.691
8	8	0.826
80	80	0.69
81	81	0.987
82	82	0.205
83	83	0.683
84	84	0.25
85	85	0.00761
86	86	0.242
87	87	0.616
88	88	0.37
89	89	0.0492
9	9	0.547
90	90	0.527
91	91	0.413
92	92	0.726
93	93	0.0509
94	94	0.693
95	95	0.559
96	96	0.373
97	97	0.538
98	98	0.209
99	99	0.502

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: CNhs10469

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011388 mouse submandibular gland- adult 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)
0007023 (adult organism)
0000922 (embryo)
0001044 (saliva-secreting gland)
0001736 (submandibular gland)
0002530 (gland)
0000033 (head)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0004121 (ectoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0005423 (developing anatomical structure)
0001444 (subdivision of head)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0003102 (surface structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0003293 (gland of oral region)
0003294 (gland of foregut)
0010047 (oral gland)
0001829 (major salivary gland)
0002365 (exocrine gland)
0003104 (mesenchyme)
0000464 (anatomical space)
0001048 (primordium)
0000925 (endoderm)
0003408 (gland of gut)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0000165 (mouth)
0007026 (primitive gut)
0001041 (foregut)
0000166 (oral opening)
0000167 (oral cavity)
0002330 (exocrine system)
0009142 (entire embryonic mesenchyme)
0000930 (stomodeum)
0006601 (presumptive ectoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0006298 (submandibular gland primordium)

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 36: / Line 36: @@
 |has_quality=
 |id=FF:59-29C1
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011388
+|is_a=EFO:0002091;;FF:0011388
+|is_obsolete=
 |name=submandibular gland, adult
 |namespace=FANTOM5
@@ Line 76: / Line 77: @@
 |sample_tissue=submandibular gland
 |top_motifs=bHLH_family:2.25156604815;FOXO1,3,4:2.21532691275;ATF6:2.21414494343;ALX1:2.18535278559;HAND1,2:2.1003865343;SNAI1..3:1.97962697295;TLX2:1.8855644112;ZEB1:1.69509924473;IRF7:1.55364747699;FOXQ1:1.5075396107;DMAP1_NCOR{1,2}_SMARC:1.49968179328;AR:1.30523994486;TP53:1.26324201346;POU2F1..3:1.22141484014;IRF1,2:0.964264841371;HIF1A:0.909510738727;ESRRA:0.896325300567;HMX1:0.861989172758;MYOD1:0.854494320147;FOXN1:0.850968670012;PAX1,9:0.75631483177;ETS1,2:0.754941205772;NFIX:0.749909384682;TEF:0.702747230169;TGIF1:0.680285652457;SP1:0.633281051965;NR1H4:0.628948518442;FOXP1:0.605216390374;XCPE1{core}:0.576078935426;HBP1_HMGB_SSRP1_UBTF:0.557498853569;SOX5:0.504005372734;LMO2:0.500386297072;ELF1,2,4:0.497527817777;ESR1:0.482468295859;DBP:0.440759305347;SPZ1:0.439813976853;FOX{D1,D2}:0.419671823365;SPIB:0.399161329776;MAFB:0.380176646938;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.378747550438;FOX{I1,J2}:0.361702452053;RUNX1..3:0.348339637292;PPARG:0.34044905856;SPI1:0.218763336517;CEBPA,B_DDIT3:0.211622437224;NFIL3:0.201724662168;MYBL2:0.165735099669;NANOG:0.134120191661;T:0.129031861783;GZF1:0.105521627411;NFATC1..3:0.0922433972573;ZBTB16:0.0872336410541;PAX4:0.0761386697432;STAT2,4,6:0.0720445265737;LHX3,4:0.068989712752;TFAP2{A,C}:0.0679886390655;TFAP4:0.0614994173314;NR6A1:0.0381291131544;REST:0.0193426482966;FOS_FOS{B,L1}_JUN{B,D}:0.0125044107009;SREBF1,2:0.0073891287437;NFKB1_REL_RELA:0.00416297896268;FOXM1:0.00174652617123;ADNP_IRX_SIX_ZHX:-0.00194251357932;GLI1..3:-0.00414123125327;FOXA2:-0.00414853896831;AIRE:-0.0219077120655;ATF2:-0.0269209597237;SRF:-0.106523087532;TEAD1:-0.115047791318;NHLH1,2:-0.130639336202;TBP:-0.138105630666;GTF2A1,2:-0.151805680559;PAX6:-0.158454998065;POU5F1:-0.160355232097;CREB1:-0.17388897593;HIC1:-0.19587369831;BPTF:-0.217265222779;NR5A1,2:-0.222517532249;CRX:-0.227281062795;STAT5{A,B}:-0.239532270756;GTF2I:-0.242609415534;ZNF148:-0.243242906762;ARID5B:-0.243564970516;PRDM1:-0.249422745871;MEF2{A,B,C,D}:-0.269136340598;NFE2L2:-0.271212961171;GCM1,2:-0.278875790051;NKX2-1,4:-0.294463444958;TFCP2:-0.300752789211;ELK1,4_GABP{A,B1}:-0.309187567698;TBX4,5:-0.310983425447;ATF5_CREB3:-0.327811079598;EP300:-0.345892547379;AHR_ARNT_ARNT2:-0.358507124249;TLX1..3_NFIC{dimer}:-0.363498158344;IKZF2:-0.366380804962;GATA4:-0.367610572311;ZNF143:-0.414108520597;MED-1{core}:-0.4144762341;OCT4_SOX2{dimer}:-0.416340327552;FOSL2:-0.417007901194;CDC5L:-0.423549406295;FOX{F1,F2,J1}:-0.423886807164;TFAP2B:-0.426523171731;HNF4A_NR2F1,2:-0.427606445533;RXRA_VDR{dimer}:-0.429239450784;FOXP3:-0.444394439562;SOX2:-0.463839514787;MYFfamily:-0.468302071007;HOXA9_MEIS1:-0.479203831943;MTF1:-0.492708825044;ZFP161:-0.497377137557;VSX1,2:-0.508527990494;BACH2:-0.512827273793;MTE{core}:-0.52290244608;NKX2-3_NKX2-5:-0.556143768129;PRRX1,2:-0.568600453746;JUN:-0.594638162582;HNF1A:-0.599644723217;GFI1:-0.602308129346;HMGA1,2:-0.603429365127;HOX{A4,D4}:-0.607907039729;POU6F1:-0.611928659423;SOX{8,9,10}:-0.614084677995;KLF4:-0.615251944119;SMAD1..7,9:-0.618253834085;NFE2L1:-0.636567105924;YY1:-0.644617074285;RFX2..5_RFXANK_RFXAP:-0.645625475973;TOPORS:-0.671595963815;RREB1:-0.671783575884;ZBTB6:-0.674046572804;POU3F1..4:-0.678539648002;NR3C1:-0.683671697317;RXR{A,B,G}:-0.69432912332;MAZ:-0.714629353659;BREu{core}:-0.723545290923;MZF1:-0.725576572297;ZNF384:-0.726713033873;FOXD3:-0.739221374773;MYB:-0.741583465574;HES1:-0.741886728065;NKX3-1:-0.750493958566;HLF:-0.759248497162;EBF1:-0.773562382382;PATZ1:-0.799839276117;RFX1:-0.803643255456;PDX1:-0.81032000792;PITX1..3:-0.821072999033;NANOG{mouse}:-0.851744965605;NRF1:-0.855666573823;GATA6:-0.857093344258;TAL1_TCF{3,4,12}:-0.861100118872;ATF4:-0.886907465347;ALX4:-0.893474819601;IKZF1:-0.937479198519;NKX6-1,2:-0.951312594015;RORA:-0.956076378782;NKX2-2,8:-0.962067026632;CDX1,2,4:-0.969509851794;PAX5:-0.975249006225;CUX2:-0.979321694116;PBX1:-1.01469801757;RBPJ:-1.05275088017;PAX2:-1.06885970668;SOX17:-1.07770760985;NFE2:-1.10136609571;POU1F1:-1.1028293371;EGR1..3:-1.11579810408;NKX3-2:-1.13180141913;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.13297427731;ONECUT1,2:-1.1489001136;NFY{A,B,C}:-1.16385414168;TFDP1:-1.19667500279;GFI1B:-1.19870026798;ZNF238:-1.21865785038;LEF1_TCF7_TCF7L1,2:-1.28909215103;E2F1..5:-1.29140751697;HOX{A5,B5}:-1.31562984483;EN1,2:-1.31995121552;UFEwm:-1.32575155526;EVI1:-1.33648886904;ZIC1..3:-1.48191610795;PAX8:-1.64159032757;FOXL1:-1.87139905138;STAT1,3:-1.92336696018;HSF1,2:-2.04425152795;ZNF423:-2.49011745673
+|xref=
 }}

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Revision as of 19:07, 27 June 2012

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