Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.11.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06126	0.901
27DAP/17DAP	1.18761	0.864
39DAP/27DAP	0.80135	0.482
41DAP/39DAP	1.86891	0.133
42DAP/41DAP	1.17597	0.958
43DAP/42DAP	0.88334	0.801
47DAP/43DAP	1.04348	0.999
52DAP/47DAP	1.93356	0.112
57DAP/52DAP	0.84587	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95983	0.352
17DAP/reference	1.04745	0.089
27DAP/reference	1.08046	0.184
39DAP/reference	1.07894	0.093
41DAP/reference	1.03039	0.421
42DAP/reference	0.97908	0.348
43DAP/reference	1.10329	0.269
47DAP/reference	0.88518	0.012
52DAP/reference	0.83665	0.082
57DAP/reference	0.88173	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98509	0.75
27DAP/17DAP	0.94389	0.854
39DAP/27DAP	1.12243	0.575
41DAP/39DAP	0.86778	0.446
42DAP/41DAP	1.26217	0.316
43DAP/42DAP	1.77222	0.013
47DAP/43DAP	1.04926	0.798
52DAP/47DAP	0.80272	0.082
57DAP/52DAP	0.91096	0.467
57DAP/7DAP	1.12605	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85649	0.086
17DAP/reference	0.84982	0.02
27DAP/reference	0.80047	0.026
39DAP/reference	0.88123	0.018
41DAP/reference	0.81276	0.017
42DAP/reference	0.79655	0.01
43DAP/reference	0.80972	0.024
47DAP/reference	0.88472	0.168
52DAP/reference	0.76524	0.057
57DAP/reference	0.7732	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0548	0.582
17DAP/reference	1.06807	0.571
27DAP/reference	0.90403	0.24
39DAP/reference	0.90001	0.227
41DAP/reference	0.83692	0.1
42DAP/reference	0.81013	0.061
43DAP/reference	1.08569	0.251
47DAP/reference	1.01468	0.965
52DAP/reference	0.96608	0.302
57DAP/reference	1.07075	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84422	0.092
17DAP/reference	0.93146	0.398
27DAP/reference	0.80453	0.032
39DAP/reference	0.79788	0.008
41DAP/reference	0.79599	0.019
42DAP/reference	0.77729	0.041
43DAP/reference	0.80076	0.037
47DAP/reference	1.01104	1
52DAP/reference	0.81262	0.18
57DAP/reference	0.57464	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98641	1
26DAP/20DAP	0.89705	0.512
34DAP/26DAP	0.93342	0.848
51DAP/34DAP	0.89201	0.264
52DAP/51DAP	1.16187	0.238
53DAP/52DAP	1.02267	0.935
55DAP/53DAP	1.06821	0.782
57DAP/55DAP	1.08977	0.947
62DAP/57DAP	1.12873	0.569
68DAP/62DAP	1.02236	0.885
68DAP/14DAP	0.9278	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38893	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99884	0.886
Mature Green Tomato/Ripe Tomato	0.6306	0.132
Immature Eggplant/Mature Eggplant	1.13198	0.248
Ripe Pepper/Ripe Tomato	0.22734	0.293
Mature Eggplant/Ripe Tomato	0.13915	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10367	0.877
1-1-2/M82	0.86724	1
12-2/M82	1.12986	1
12-4/M82	0.98674	1
1-3/M82	0.97076
2-1-1/M82	1.141	1
2-1/M82	0.95071	1
2-6/M82	1.08825	1
3-2/M82	1.07332	0.463
4-1-1/M82	1.05922	1
4-1/M82	0.91062	1
4-3-2/M82	1.13576	0.284
4-3/M82	0.95756	1
5-3/M82	1.03345	0.572
6-2/M82	0.95789	1
6-3/M82	0.9259	0.857
7-1/M82	0.81105
7-2/M82	1.09068	1
9-3-2/M82	1.36025	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97973	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.93122	1
IL12-4/WTpooled	1.19251	0.673
IL1-4/WTpooled	0.90612	0.699
WT/WTpooled	1.1218	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.03872	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03883	0.921
DC3000/delta hrp 6h	1.11859	1
DC3000/delta hrp 12h	1.14997	1
DC3000/delta hrp 24h	0.94847	0.534

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.94797	0.657

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91061	0.265
Exp 36h	1.12725	0.693
Exp 60h	0.95978	0.586

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.95076	1
Var 0h	2.61973	0.936
Var 12h I row2-row1	1.04576	0.613
Var 12h NI row2-row1	0.77416	0.466
Var 36h I row2-row1	0.82235	0.805
Var 36h NI row2-row1	1.23835	1
Var 60h I row2-row1	1.26758	0.562
Var 60h NI row2-row1	1.28996	0.904
Time course 0hI-0hNI	1.14563	0.537
Time course 12hI-12hNI	1.06872	0.639
Time course 36hI-36hNI	0.93726	0.027
Time course 60hI-60hNI	1.24781	0.019

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.00589	0.931
transgenic ySAMdc/azygous control (breaker)	0.80515	0.15
transgenic ySAMdc/azygous control (red)	1.68683	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01385	0.287

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0161	1

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75867	1
Manapal/WT (break)	1.44494	1
Manapal/WT (red)	0.84579	0.181