Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27766	0.452
27DAP/17DAP	0.48769	0.031
39DAP/27DAP	0.66873	0.326
41DAP/39DAP	0.61315	0.053
42DAP/41DAP	0.67675	0.774
43DAP/42DAP	1.06575	1
47DAP/43DAP	0.69916	0.185
52DAP/47DAP	1.07137	0.957
57DAP/52DAP	1.12205	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70904	0.064
17DAP/reference	0.49959	0.008
27DAP/reference	0.49665	0.012
39DAP/reference	0.36278	0.01
41DAP/reference	0.25342	0.008
42DAP/reference	0.34049	0.001
43DAP/reference	0.19874	0.012
47DAP/reference	0.2279	0.001
52DAP/reference	0.26232	0.01
57DAP/reference	0.24255	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.66713	0.036
27DAP/17DAP	0.7212	0.131
39DAP/27DAP	0.50018	0.028
41DAP/39DAP	1.1146	0.455
42DAP/41DAP	1.08281	0.55
43DAP/42DAP	0.69392	0.022
47DAP/43DAP	0.8477	0.153
52DAP/47DAP	2.21782	0.048
57DAP/52DAP	2.50274	0.035
57DAP/7DAP	1.41102	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04481	0.638
17DAP/reference	0.78401	0.02
27DAP/reference	0.55712	0.01
39DAP/reference	0.41124	0.011
41DAP/reference	0.34415	0.009
42DAP/reference	0.3193	0.01
43DAP/reference	0.24771	0.009
47DAP/reference	0.24876	0.026
52DAP/reference	0.31908	0.009
57DAP/reference	0.38011	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42144	0.007
17DAP/reference	0.49608	0.014
27DAP/reference	0.6321	0.054
39DAP/reference	0.31087	0.008
41DAP/reference	0.43142	0.006
42DAP/reference	0.49078	0.017
43DAP/reference	0.20172	0.002
47DAP/reference	0.34208	0.01
52DAP/reference	0.23442	0.003
57DAP/reference	0.09845	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.1798	0.016
17DAP/reference	1.99944	0.102
27DAP/reference	1.48016	0.038
39DAP/reference	1.1403	0.342
41DAP/reference	0.70475	0.025
42DAP/reference	0.52596	0.014
43DAP/reference	0.50975	0.018
47DAP/reference	0.25297	0.005
52DAP/reference	0.31139	0.047
57DAP/reference	1.23657	0.452

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05067	1
26DAP/20DAP	0.99814	1
34DAP/26DAP	1.40273	1
51DAP/34DAP	0.64494	0.108
52DAP/51DAP	3.45509	0.034
53DAP/52DAP	0.65936	0.051
55DAP/53DAP	1.59303	0.044
57DAP/55DAP	0.30823	0.025
62DAP/57DAP	1.98583	0.029
68DAP/62DAP	2.13077	0.89
68DAP/14DAP	0.43628	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.19864	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.99891	0.058
Mature Green Tomato/Ripe Tomato	13.3226	0.015
Immature Eggplant/Mature Eggplant	0.42873	0.058
Ripe Pepper/Ripe Tomato	19.1659	0.239
Mature Eggplant/Ripe Tomato	57.883	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10901	1
1-1-2/M82	N/A	N/A
12-2/M82	0.58492
12-4/M82	1.20805
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	1.06229
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.26674	1
6-2/M82	0.35927
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.83505
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21967	0.277
IL2-6/WTpooled	1.00452	1
IL7-5/WTpooled	1.07454
IL7-3/WTpooled	1.05712	1
IL12-4/WTpooled	1.09812	0.673
IL1-4/WTpooled	1.10783
WT/WTpooled	0.93925	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	0.90292	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9419	1
DC3000/delta hrp 6h	0.93865	0.95
DC3000/delta hrp 12h	1.33849	1
DC3000/delta hrp 24h	0.99805	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88273
DC3000 delta B/DC3000 delta AB	0.81648	0.065

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16768	1
Exp 36h	0.98773	0.943
Exp 60h	0.83801	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06016	1
Var 0h	0.54015	1
Var 12h I row2-row1	1.16351	0.406
Var 12h NI row2-row1	1.02831	1
Var 36h I row2-row1	0.98041	1
Var 36h NI row2-row1	1.70769	1
Var 60h I row2-row1	1.61788	0.562
Var 60h NI row2-row1	1.04928	0.904
Time course 0hI-0hNI	1.0402	0.852
Time course 12hI-12hNI	1.03668	0.798
Time course 36hI-36hNI	1.07484	0.28
Time course 60hI-60hNI	0.58312	0.026

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)	1.08619	0.921
transgenic ySAMdc/azygous control (breaker)	4.96938	0.162
transgenic ySAMdc/azygous control (red)	1.62528	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.57137	0.075

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.6702	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	22.6212	0.084
Manapal/WT (break)	19.0965	0.126
Manapal/WT (red)	4.87898	0.413