Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.14.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14998	0.739
27DAP/17DAP	0.57576	0.046
39DAP/27DAP	0.74416	0.41
41DAP/39DAP	0.85204	0.43
42DAP/41DAP	0.93895	1
43DAP/42DAP	0.96468	0.91
47DAP/43DAP	0.72842	0.251
52DAP/47DAP	2.15853	0.156
57DAP/52DAP	0.57547	0.613

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30679	0.35
17DAP/reference	1.11413	0.258
27DAP/reference	0.79017	0.137
39DAP/reference	0.77107	0.035
41DAP/reference	0.79325	0.085
42DAP/reference	0.96676	0.295
43DAP/reference	0.48978	0.017
47DAP/reference	0.69408	0.001
52DAP/reference	0.52816	0.014
57DAP/reference	0.62301	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.14716	0.036
27DAP/17DAP	0.70482	0.172
39DAP/27DAP	0.43461	0.031
41DAP/39DAP	1.33568	0.028
42DAP/41DAP	0.83379	0.064
43DAP/42DAP	0.60373	0.022
47DAP/43DAP	0.96306	0.857
52DAP/47DAP	1.03625	0.947
57DAP/52DAP	0.84116	0.209
57DAP/7DAP	0.21572	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14122	0.318
17DAP/reference	0.97951	0.447
27DAP/reference	0.89244	0.035
39DAP/reference	0.77928	0.012
41DAP/reference	0.72774	0.01
42DAP/reference	0.66065	0.01
43DAP/reference	0.73353	0.025
47DAP/reference	0.77679	0.168
52DAP/reference	0.78874	0.077
57DAP/reference	0.68224	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32945	0.11
17DAP/reference	1.91424	0.007
27DAP/reference	1.27492	0.26
39DAP/reference	1.00064	0.642
41DAP/reference	1.0166	0.749
42DAP/reference	1.3497	0.009
43DAP/reference	0.72161	0.125
47DAP/reference	1.00149	0.812
52DAP/reference	0.74522	0.018
57DAP/reference	0.70482	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.97574	0.022
17DAP/reference	1.66785	0.088
27DAP/reference	1.36335	0.028
39DAP/reference	1.28663	0.035
41DAP/reference	0.98196	0.56
42DAP/reference	0.95227	0.445
43DAP/reference	0.92116	0.179
47DAP/reference	0.51948	0.007
52DAP/reference	0.79717	0.169
57DAP/reference	0.97522	0.553

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.56845	0.407
26DAP/20DAP	1.14716	0.806
34DAP/26DAP	0.93179	0.861
51DAP/34DAP	0.50548	0.059
52DAP/51DAP	0.98875	1
53DAP/52DAP	0.66095	0.05
55DAP/53DAP	0.78964	0.046
57DAP/55DAP	0.98028	0.795
62DAP/57DAP	1.08085	0.935
68DAP/62DAP	0.79291	0.543
68DAP/14DAP	0.68114	0.075

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.35775	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.53157	0.075
Mature Green Tomato/Ripe Tomato	13.1252	0.016
Immature Eggplant/Mature Eggplant	0.56148	0.057
Ripe Pepper/Ripe Tomato	32.2805
Mature Eggplant/Ripe Tomato	45.7622	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86881	0.907
1-1-2/M82	0.83151	1
12-2/M82	0.93149	0.721
12-4/M82	0.86735	1
1-3/M82	1.03871	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.86024
3-2/M82	0.96553	0.752
4-1-1/M82	1.07937	1
4-1/M82	0.93433	1
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.26223	0.572
6-2/M82	0.90056	1
6-3/M82	1.00347	1
7-1/M82	N/A	N/A
7-2/M82	1.08501	1
9-3-2/M82	0.81246	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00764
IL2-6/WTpooled	0.98479	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.22094	1
IL12-4/WTpooled	0.95401	1
IL1-4/WTpooled	1.15627
WT/WTpooled	0.98392	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	0.8857	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90596	1
DC3000/delta hrp 6h	1.21627	1
DC3000/delta hrp 12h	1.22528	1
DC3000/delta hrp 24h	0.9851	0.966

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.83149	0.027
DC3000 delta B/DC3000 delta AB	0.48809	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08862	1
Exp 36h	0.82709	0.699
Exp 60h	0.96338	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10236	1
Var 0h	1.02276	1
Var 12h I row2-row1	1.16336	0.58
Var 12h NI row2-row1	0.95637	0.906
Var 36h I row2-row1	1.23221	1
Var 36h NI row2-row1	1.44275	1
Var 60h I row2-row1	1.49029	0.562
Var 60h NI row2-row1	0.93555	0.977
Time course 0hI-0hNI	1.0666	0.852
Time course 12hI-12hNI	1.03409	0.867
Time course 36hI-36hNI	1.05997	0.722
Time course 60hI-60hNI	0.33837	0.011

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)	1.13102	0.325
transgenic ySAMdc/azygous control (breaker)	1.12996	1
transgenic ySAMdc/azygous control (red)	1.16923	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84089	0.242

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.7949	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.35018	0.084
Manapal/WT (break)	1.33698	0.381
Manapal/WT (red)	2.8539	0.413