Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.9.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44546	0.219
27DAP/17DAP	1.56574	0.588
39DAP/27DAP	4.27046	0.358
41DAP/39DAP	1.8597	0.56
42DAP/41DAP	1.10409	1
43DAP/42DAP	1.27878	0.999
47DAP/43DAP	0.33508	0.049
52DAP/47DAP	0.92506	0.72
57DAP/52DAP	1.42832	0.694

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73995	0.064
17DAP/reference	0.75675	0.031
27DAP/reference	0.83767	0.124
39DAP/reference	0.77754	0.037
41DAP/reference	0.74396	0.085
42DAP/reference	1.41306	0.026
43DAP/reference	0.85838	0.107
47DAP/reference	0.78423	0.006
52DAP/reference	0.74326	0.043
57DAP/reference	1.00405	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55246	0.105
27DAP/17DAP	0.97953	0.919
39DAP/27DAP	3.56808	0.04
41DAP/39DAP	4.44557	0.005
42DAP/41DAP	0.59012	0.007
43DAP/42DAP	0.40019	0.022
47DAP/43DAP	1.07008	0.779
52DAP/47DAP	1.34459	0.915
57DAP/52DAP	0.62336	0.264
57DAP/7DAP	1.30037	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74981	0.073
17DAP/reference	1.8007	0.199
27DAP/reference	2.03815	0.16
39DAP/reference	1.44754	0.186
41DAP/reference	0.92492	0.284
42DAP/reference	1.75163	0.132
43DAP/reference	1.24462	0.637
47DAP/reference	1.80671	0.065
52DAP/reference	2.02139	0.01
57DAP/reference	2.27078	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66692	0.006
17DAP/reference	0.72217	0.004
27DAP/reference	0.81755	0.033
39DAP/reference	1.73852	0.225
41DAP/reference	0.96626	0.393
42DAP/reference	1.50201	0.38
43DAP/reference	3.58267	0.04
47DAP/reference	3.88326	0.008
52DAP/reference	1.07087	0.667
57DAP/reference	3.05783	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90382	0.311
17DAP/reference	1.18245	0.876
27DAP/reference	0.76271	0.046
39DAP/reference	1.39853	0.163
41DAP/reference	1.45797	0.069
42DAP/reference	0.90424	0.287
43DAP/reference	0.6817	0.037
47DAP/reference	0.69947	0.008
52DAP/reference	0.9217	0.518
57DAP/reference	0.71797	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27715	0.966
26DAP/20DAP	1.21716	0.813
34DAP/26DAP	1.06879	1
51DAP/34DAP	1.17987	0.967
52DAP/51DAP	0.54288	0.079
53DAP/52DAP	1.11671	0.929
55DAP/53DAP	1.00753	0.917
57DAP/55DAP	1.14616	0.935
62DAP/57DAP	1.07885	1
68DAP/62DAP	0.923	0.747
68DAP/14DAP	1.06958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.78073	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	11.7348	0.032
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.22933
Mature Eggplant/Ripe Tomato	0.19846	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.13671
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.96982
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.74272
7-2/M82	N/A	N/A
9-3-2/M82	1.49941	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.0501	0.788
IL7-5/WTpooled	0.31764
IL7-3/WTpooled	0.73849	0.31
IL12-4/WTpooled	1.06113	0.785
IL1-4/WTpooled	0.94046	0.834
WT/WTpooled	1.14515	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	1.8613	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.26386	0.921
DC3000/delta hrp 6h	1.06285	0.978
DC3000/delta hrp 12h	1.27257	1
DC3000/delta hrp 24h	2.46553	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.39532	0.042
DC3000 delta B/DC3000 delta AB	5.09584	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	2.0782	0.201
Exp 36h	1.51319	0.693
Exp 60h	3.46787	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96756	1
Var 0h	1.10256	1
Var 12h I row2-row1	0.99119	1
Var 12h NI row2-row1	2.57278	0.161
Var 36h I row2-row1	1.70444	0.489
Var 36h NI row2-row1	0.43966	0.478
Var 60h I row2-row1	1.01768	1
Var 60h NI row2-row1	0.6603	0.483
Time course 0hI-0hNI	1.81538	0.63
Time course 12hI-12hNI	1.62652	0.611
Time course 36hI-36hNI	11.9742	0.004
Time course 60hI-60hNI	218.545	0.008

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)	0.45934	0.246
transgenic ySAMdc/azygous control (breaker)	0.99519	1
transgenic ySAMdc/azygous control (red)	0.84353	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00682	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.25098	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8453	1
Manapal/WT (break)	0.56371	0.333
Manapal/WT (red)	0.64515	0.242