Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.4.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74133	0.069
27DAP/17DAP	0.58237	0.045
39DAP/27DAP	0.85012	0.447
41DAP/39DAP	1.06626	0.887
42DAP/41DAP	0.60357	0.262
43DAP/42DAP	0.86469	0.717
47DAP/43DAP	0.87152	0.584
52DAP/47DAP	1.19431	0.994
57DAP/52DAP	0.74983	0.71

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01664	0.771
17DAP/reference	1.33975	0.051
27DAP/reference	1.32301	0.014
39DAP/reference	0.99686	0.921
41DAP/reference	1.03902	0.808
42DAP/reference	0.76409	0.001
43DAP/reference	0.8143	0.058
47DAP/reference	0.7965	0.001
52DAP/reference	0.84309	0.105
57DAP/reference	0.90443	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.41465	0.027
27DAP/17DAP	1.0998	0.645
39DAP/27DAP	0.69463	0.032
41DAP/39DAP	1.13966	0.65
42DAP/41DAP	0.99711	0.841
43DAP/42DAP	0.82028	0.054
47DAP/43DAP	0.9463	0.781
52DAP/47DAP	1.05663	0.816
57DAP/52DAP	0.87013	0.294
57DAP/7DAP	0.4843	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04849	1
17DAP/reference	1.04136	0.971
27DAP/reference	0.96798	0.494
39DAP/reference	1.29507	0.175
41DAP/reference	1.29237	0.045
42DAP/reference	1.26113	0.1
43DAP/reference	1.09455	0.788
47DAP/reference	0.91445	0.293
52DAP/reference	1.19327	0.092
57DAP/reference	1.02196	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93062	0.564
17DAP/reference	1.40548	0.052
27DAP/reference	1.02437	0.765
39DAP/reference	0.9867	0.569
41DAP/reference	0.98269	0.557
42DAP/reference	1.13536	0.408
43DAP/reference	0.8318	0.236
47DAP/reference	0.78648	0.032
52DAP/reference	0.73828	0.22
57DAP/reference	0.62001	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04579	0.864
17DAP/reference	0.993	0.778
27DAP/reference	1.0912	0.552
39DAP/reference	1.06318	0.633
41DAP/reference	1.19004	0.188
42DAP/reference	0.98132	0.671
43DAP/reference	0.97242	0.523
47DAP/reference	0.73343	0.009
52DAP/reference	0.97099	0.704
57DAP/reference	1.0627	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89189	0.997
26DAP/20DAP	1.03368	1
34DAP/26DAP	0.76332	0.399
51DAP/34DAP	0.79486	0.385
52DAP/51DAP	0.86297	1
53DAP/52DAP	0.58951	0.133
55DAP/53DAP	1.27589	0.361
57DAP/55DAP	0.8838	0.633
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.70533	0.331
68DAP/14DAP	0.74442	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04544	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	35.9722	0.058
Mature Green Tomato/Ripe Tomato	5.70218	0.015
Immature Eggplant/Mature Eggplant	0.12082	0.057
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	8.912	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96763
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.84861	0.619
1-3/M82	0.8727
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	0.98309
4-3/M82	N/A	N/A
5-3/M82	0.83512	0.49
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	0.69464

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.85817
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08069	1
IL12-4/WTpooled	0.90282	1
IL1-4/WTpooled	1.13354
WT/WTpooled	1.21013	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	0.7031	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99575	1
DC3000/delta hrp 6h	1.01344	0.95
DC3000/delta hrp 12h	0.90554	1
DC3000/delta hrp 24h	0.60928	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8662	0.047
DC3000 delta B/DC3000 delta AB	0.82538	0.21

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1054	1
Exp 36h	0.87177	0.699
Exp 60h	1.09289	1

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	N/A	N/A
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)	1.15278	0.292
transgenic ySAMdc/azygous control (breaker)	0.67817	0.15
transgenic ySAMdc/azygous control (red)	1.07139	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97295	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03008	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93496	1
Manapal/WT (break)	1.23768	1
Manapal/WT (red)	N/A	N/A