Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68149	0.032
27DAP/17DAP	0.81511	0.542
39DAP/27DAP	1.26952	0.473
41DAP/39DAP	0.71777	0.121
42DAP/41DAP	0.69973	0.774
43DAP/42DAP	1.06964	1
47DAP/43DAP	0.48412	0.049
52DAP/47DAP	1.15098	0.828
57DAP/52DAP	1.41435	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77731	0.018
17DAP/reference	1.06523	0.904
27DAP/reference	0.63423	0.012
39DAP/reference	0.70249	0.044
41DAP/reference	0.70929	0.039
42DAP/reference	1.18063	0.05
43DAP/reference	0.74052	0.015
47DAP/reference	0.78998	0.001
52DAP/reference	0.48379	0.013
57DAP/reference	0.63825	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87138	0.201
27DAP/17DAP	1.10273	0.587
39DAP/27DAP	0.79124	0.066
41DAP/39DAP	1.01519	0.973
42DAP/41DAP	1.02038	1
43DAP/42DAP	0.93856	0.558
47DAP/43DAP	0.94951	0.781
52DAP/47DAP	0.58358	0.044
57DAP/52DAP	0.87459	0.448
57DAP/7DAP	0.21274	0.159

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.58993	0.024
17DAP/reference	2.00221	0.006
27DAP/reference	1.48485	0.008
39DAP/reference	1.30278	0.008
41DAP/reference	1.35524	0.014
42DAP/reference	1.23889	0.059
43DAP/reference	1.14552	0.178
47DAP/reference	1.08186	0.761
52DAP/reference	1.1679	0.212
57DAP/reference	0.92891	0.24

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21758	0.404
17DAP/reference	1.55835	0.012
27DAP/reference	1.43907	0.04
39DAP/reference	0.83523	0.031
41DAP/reference	1.11722	0.362
42DAP/reference	1.4073	0.012
43DAP/reference	0.84834	0.152
47DAP/reference	1.15311	0.12
52DAP/reference	0.59876	0.005
57DAP/reference	0.70568	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.09509	0.016
17DAP/reference	1.45756	0.224
27DAP/reference	1.53569	0.03
39DAP/reference	1.56005	0.011
41DAP/reference	1.16979	0.031
42DAP/reference	1.14139	0.226
43DAP/reference	1.23061	0.254
47DAP/reference	0.50702	0.004
52DAP/reference	0.99224	0.763
57DAP/reference	0.83168	0.136

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31068	0.966
26DAP/20DAP	4.92897	0.097
34DAP/26DAP	0.65327	0.078
51DAP/34DAP	0.90922	0.532
52DAP/51DAP	0.90116	1
53DAP/52DAP	0.75172	0.173
55DAP/53DAP	0.82596	0.022
57DAP/55DAP	1.09788	0.87
62DAP/57DAP	0.97565	0.994
68DAP/62DAP	0.78851	0.211
68DAP/14DAP	1.1739	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.05775	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98307	0.805
Mature Green Tomato/Ripe Tomato	2.55332	0.038
Immature Eggplant/Mature Eggplant	0.86961	0.086
Ripe Pepper/Ripe Tomato	1.50889	0.258
Mature Eggplant/Ripe Tomato	1.80545	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01395	1
1-1-2/M82	1.2001	1
12-2/M82	0.87033	0.955
12-4/M82	1.11234	1
1-3/M82	1.31512	1
2-1-1/M82	1.07483	1
2-1/M82	1.28081	1
2-6/M82	1.16777	0.594
3-2/M82	0.89809
4-1-1/M82	2.22367
4-1/M82	1.67312	0.853
4-3-2/M82	2.24057	0.284
4-3/M82	1.43425	0.268
5-3/M82	1.29491	0.378
6-2/M82	N/A	N/A
6-3/M82	0.7339	0.982
7-1/M82	1.10389	1
7-2/M82	1.58597	0.291
9-3-2/M82	1.51179	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.58098	0.277
IL2-6/WTpooled	0.99403	1
IL7-5/WTpooled	0.38182
IL7-3/WTpooled	0.96401	1
IL12-4/WTpooled	1.06273	0.695
IL1-4/WTpooled	1.05008	1
WT/WTpooled	0.92736	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	1.14929	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97664	1
DC3000/delta hrp 6h	1.04835	1
DC3000/delta hrp 12h	1.14979	1
DC3000/delta hrp 24h	1.05821	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44138
DC3000 delta B/DC3000 delta AB	1.35386	0.151

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20485	1
Exp 36h	1.00829	1
Exp 60h	1.14032	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9997	1
Var 0h	0.83507	0.933
Var 12h I row2-row1	0.93208	0.705
Var 12h NI row2-row1	1.07968	1
Var 36h I row2-row1	0.95475	1
Var 36h NI row2-row1	0.97144	0.706
Var 60h I row2-row1	0.87726	0.285
Var 60h NI row2-row1	0.87734	0.756
Time course 0hI-0hNI	1.10101	0.603
Time course 12hI-12hNI	1.02292	0.811
Time course 36hI-36hNI	1.40588	0.016
Time course 60hI-60hNI	1.37751	0.012

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)	1.04912	0.748
transgenic ySAMdc/azygous control (breaker)	1.1025	1
transgenic ySAMdc/azygous control (red)	1.27195	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2613	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91122	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08824	0.307
Manapal/WT (break)	1.05939	0.381
Manapal/WT (red)	0.92852	0.199