Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.12.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10089	0.532
27DAP/17DAP	1.27801	0.982
39DAP/27DAP	1.64003	0.14
41DAP/39DAP	1.05195	0.758
42DAP/41DAP	0.96517	1
43DAP/42DAP	1.27611	0.671
47DAP/43DAP	1.1553	0.842
52DAP/47DAP	2.24399	0.637
57DAP/52DAP	1.30656	0.843

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22358	0.35
17DAP/reference	0.66619	0.035
27DAP/reference	0.71959	0.057
39DAP/reference	0.58614	0.021
41DAP/reference	0.50018	0.01
42DAP/reference	0.88236	0.072
43DAP/reference	0.60738	0.015
47DAP/reference	0.60397	0.001
52DAP/reference	0.43001	0.013
57DAP/reference	0.6202	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	0.95672	0.919
39DAP/27DAP	1.6974	0.28
41DAP/39DAP	1.56821
42DAP/41DAP	2.5065	0.263
43DAP/42DAP	0.99894	1
47DAP/43DAP	0.68645	0.743
52DAP/47DAP	1.96135	0.424
57DAP/52DAP	2.73168	0.243
57DAP/7DAP	1.16599	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.34573	0.024
17DAP/reference	2.34577	0.006
27DAP/reference	1.41397	0.026
39DAP/reference	1.34258	0.007
41DAP/reference	1.17595	1
42DAP/reference	1.29378	0.037
43DAP/reference	1.42445	0.02
47DAP/reference	0.77336	0.222
52DAP/reference	1.63787	0.021
57DAP/reference	1.51839	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94129	0.412
17DAP/reference	0.65398	0.012
27DAP/reference	0.89619	0.304
39DAP/reference	0.62558	0.016
41DAP/reference	0.99093	0.493
42DAP/reference	0.70752	0.013
43DAP/reference	0.33738	0.005
47DAP/reference	0.56163	0.012
52DAP/reference	0.37926	0.003
57DAP/reference	0.26619	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.58435	0.015
17DAP/reference	2.29692	0.146
27DAP/reference	2.89051	0.019
39DAP/reference	3.04707	0.012
41DAP/reference	1.99087	0.012
42DAP/reference	1.75004	0.035
43DAP/reference	1.45703	0.077
47DAP/reference	0.46014	0.004
52DAP/reference	1.25088	0.714
57DAP/reference	0.96811	0.483

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15863	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	3.06393	0.819
51DAP/34DAP	0.82115	0.667
52DAP/51DAP	0.5098
53DAP/52DAP	1.92819	0.171
55DAP/53DAP	1.25802	0.366
57DAP/55DAP	0.64997	0.144
62DAP/57DAP	0.91964	0.871
68DAP/62DAP	2.22623	0.126
68DAP/14DAP	4.31409	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.93838	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.06941	0.898
Immature Eggplant/Mature Eggplant	2.10823	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.10659	1
12-2/M82	N/A	N/A
12-4/M82	1.85053
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	1.38947
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.21217	0.262
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	0.82745
7-2/M82	N/A	N/A
9-3-2/M82	1.87338	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13216
IL2-6/WTpooled	0.79505
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.90803
IL12-4/WTpooled	0.75812	0.581
IL1-4/WTpooled	1.08103
WT/WTpooled	0.8479	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	5.31969	1
DC3000/delta hrp 6h	0.71677	0.942
DC3000/delta hrp 12h	0.64962	1
DC3000/delta hrp 24h	8.44549	1

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08819	1
Exp 36h	3.74611	1
Exp 60h	1.51903	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.08736	0.259
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.81621	0.218
transgenic ySAMdc/azygous control (breaker)	0.74064	0.173
transgenic ySAMdc/azygous control (red)	1.55785	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11569	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.60391	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.87358	1
Manapal/WT (break)	1.77306	0.381
Manapal/WT (red)	1.38273	0.126