Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.12.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90347	0.551
27DAP/17DAP	1.03947	0.905
39DAP/27DAP	1.42885	0.344
41DAP/39DAP	0.82048	0.357
42DAP/41DAP	1.20451	0.813
43DAP/42DAP	0.90506	0.77
47DAP/43DAP	0.90369	0.671
52DAP/47DAP	0.80339	0.476
57DAP/52DAP	1.08459	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3023	0.038
17DAP/reference	1.31825	0.016
27DAP/reference	1.23154	0.098
39DAP/reference	1.18941	0.058
41DAP/reference	1.44222	0.014
42DAP/reference	1.56203	0.001
43DAP/reference	1.15825	0.025
47DAP/reference	1.34795	0.001
52DAP/reference	1.31738	0.069
57DAP/reference	1.04784	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02372	1
27DAP/17DAP	1.14662	0.373
39DAP/27DAP	1.14221	0.512
41DAP/39DAP	1.05762	0.727
42DAP/41DAP	1.0849	0.308
43DAP/42DAP	0.85086	0.056
47DAP/43DAP	1.02347	0.99
52DAP/47DAP	1.71905	0.068
57DAP/52DAP	1.5739	0.055
57DAP/7DAP	2.55414	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.89194	0.026
17DAP/reference	1.23207	0.022
27DAP/reference	1.16669	0.03
39DAP/reference	1.2232	0.015
41DAP/reference	1.25036	0.013
42DAP/reference	1.31426	0.03
43DAP/reference	1.11013	0.344
47DAP/reference	1.349	0.023
52DAP/reference	1.01836	1
57DAP/reference	0.9578	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31796	0.495
17DAP/reference	1.63904	0.026
27DAP/reference	1.26677	0.143
39DAP/reference	1.49998	0.012
41DAP/reference	1.60329	0.005
42DAP/reference	1.62966	0.008
43DAP/reference	1.16046	0.899
47DAP/reference	1.22493	0.095
52DAP/reference	1.29209	0.024
57DAP/reference	1.35944	0.033

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.15365	0.02
17DAP/reference	1.51864	0.09
27DAP/reference	1.53033	0.021
39DAP/reference	1.2199	0.048
41DAP/reference	1.20614	0.265
42DAP/reference	1.21155	0.068
43DAP/reference	1.33937	0.285
47DAP/reference	1.41686	0.02
52DAP/reference	1.26124	0.119
57DAP/reference	1.37983	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.70924	0.033
26DAP/20DAP	2.01321	0.518
34DAP/26DAP	2.06021	1
51DAP/34DAP	1.18515	0.962
52DAP/51DAP	3.00814	0.034
53DAP/52DAP	0.75743	0.122
55DAP/53DAP	1.71505	0.042
57DAP/55DAP	0.60102	0.057
62DAP/57DAP	1.0118	0.994
68DAP/62DAP	1.62454	0.872
68DAP/14DAP	1.26112	0.2

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64395	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00367	0.863
Mature Green Tomato/Ripe Tomato	1.15128	0.299
Immature Eggplant/Mature Eggplant	1.01492	0.633
Ripe Pepper/Ripe Tomato	0.63893	0.224
Mature Eggplant/Ripe Tomato	0.91166

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.53465
12-2/M82	N/A	N/A
12-4/M82	1.24741	1
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	0.89843
4-1-1/M82	N/A	N/A
4-1/M82	2.2281
4-3-2/M82	1.22666
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.90561
7-2/M82	N/A	N/A
9-3-2/M82	1.27663	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.9468

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	1.18651	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86945	1
DC3000/delta hrp 6h	0.8701	0.95
DC3000/delta hrp 12h	1.16294	1
DC3000/delta hrp 24h	0.73656	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9102	0.093
DC3000 delta B/DC3000 delta AB	0.95767	0.543

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14862	1
Exp 36h	0.84581	0.471
Exp 60h	1.07125	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96822	1
Var 0h	0.68225	1
Var 12h I row2-row1	0.81456	0.39
Var 12h NI row2-row1	0.99776	1
Var 36h I row2-row1	0.96464	1
Var 36h NI row2-row1	1.04929	1
Var 60h I row2-row1	0.9978	1
Var 60h NI row2-row1	0.92259	0.977
Time course 0hI-0hNI	0.99578	1
Time course 12hI-12hNI	1.0884	0.647
Time course 36hI-36hNI	1.14971	0.025
Time course 60hI-60hNI	1.26375	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)	0.98946	0.789
transgenic ySAMdc/azygous control (breaker)	0.98319	1
transgenic ySAMdc/azygous control (red)	1.12015	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99349	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94117	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05221	0.307
Manapal/WT (break)	1.03884	1
Manapal/WT (red)	1.14019	0.413