Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.2.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15554	0.681
27DAP/17DAP	0.51033	0.039
39DAP/27DAP	0.63169	0.278
41DAP/39DAP	0.93469	0.73
42DAP/41DAP	0.76939	0.774
43DAP/42DAP	0.92236	0.865
47DAP/43DAP	0.70554	0.225
52DAP/47DAP	1.15291	0.945
57DAP/52DAP	1.30643	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66079	0.027
17DAP/reference	0.61441	0.01
27DAP/reference	0.66676	0.032
39DAP/reference	0.65206	0.021
41DAP/reference	0.52273	0.01
42DAP/reference	0.70462	0.002
43DAP/reference	0.81241	0.135
47DAP/reference	0.74972	0.008
52DAP/reference	0.72495	0.096
57DAP/reference	0.98959	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99167	0.801
27DAP/17DAP	0.8339	0.475
39DAP/27DAP	0.47642	0.028
41DAP/39DAP	1.19542	0.656
42DAP/41DAP	0.88985	0.156
43DAP/42DAP	0.69975	0.032
47DAP/43DAP	0.90532	0.439
52DAP/47DAP	0.97327	0.905
57DAP/52DAP	1.01467	0.869
57DAP/7DAP	0.47629	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87782	0.069
17DAP/reference	0.83997	0.011
27DAP/reference	0.78306	0.01
39DAP/reference	0.88583	0.016
41DAP/reference	0.75901	0.022
42DAP/reference	0.8213	0.012
43DAP/reference	0.84196	0.013
47DAP/reference	0.6459	0.057
52DAP/reference	0.79974	0.027
57DAP/reference	0.83523	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59134	0.01
17DAP/reference	0.55436	0.008
27DAP/reference	0.6242	0.014
39DAP/reference	0.63054	0.041
41DAP/reference	0.67304	0.012
42DAP/reference	0.55359	0.012
43DAP/reference	0.65345	0.03
47DAP/reference	0.67074	0.011
52DAP/reference	0.46071	0.003
57DAP/reference	0.35319	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87117	0.05
17DAP/reference	1.02953	0.977
27DAP/reference	0.78793	0.025
39DAP/reference	0.73611	0.014
41DAP/reference	0.83329	0.03
42DAP/reference	0.7873	0.071
43DAP/reference	0.79034	0.028
47DAP/reference	0.57908	0.006
52DAP/reference	0.59503	0.066
57DAP/reference	0.75142	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07749	0.966
26DAP/20DAP	0.88813	0.512
34DAP/26DAP	0.87004	0.561
51DAP/34DAP	0.56561	0.063
52DAP/51DAP	1.02886	0.836
53DAP/52DAP	1.10934	0.738
55DAP/53DAP	1.00261	0.864
57DAP/55DAP	0.98234	0.909
62DAP/57DAP	0.98081	0.994
68DAP/62DAP	1.23617	0.589
68DAP/14DAP	1.00142	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85873	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.08135	0.058
Mature Green Tomato/Ripe Tomato	10.1195	0.015
Immature Eggplant/Mature Eggplant	0.41108	0.062
Ripe Pepper/Ripe Tomato	2.85705
Mature Eggplant/Ripe Tomato	16.6662	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.00752
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.15462	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.37855	0.277
IL2-6/WTpooled	0.54129	0.348
IL7-5/WTpooled	0.77861	1
IL7-3/WTpooled	1.76333	1
IL12-4/WTpooled	0.90349	1
IL1-4/WTpooled	1.09379	1
WT/WTpooled	1.07484	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	1.03139	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95164	1
DC3000/delta hrp 6h	1.18919	1
DC3000/delta hrp 12h	0.87281	1
DC3000/delta hrp 24h	0.93964	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.40647	0.025
DC3000 delta B/DC3000 delta AB	0.33409	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93296	1
Exp 36h	0.68267	0.456
Exp 60h	0.52732	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98061	1
Var 0h	1.05555	0.98
Var 12h I row2-row1	0.69556	0.363
Var 12h NI row2-row1	0.96589	0.906
Var 36h I row2-row1	0.76189	0.575
Var 36h NI row2-row1	1.08016	1
Var 60h I row2-row1	1.29414	0.543
Var 60h NI row2-row1	1.03966	1
Time course 0hI-0hNI	0.94731	0.721
Time course 12hI-12hNI	1.08692	0.703
Time course 36hI-36hNI	0.75657	0.047
Time course 60hI-60hNI	0.08049	0.005

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)	1.11662	0.748
transgenic ySAMdc/azygous control (breaker)	1.66668	0.178
transgenic ySAMdc/azygous control (red)	1.26431	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.54905	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.0483	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	8.90811	0.087
Manapal/WT (break)	6.45993	0.123
Manapal/WT (red)	1.20707	1