Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.19.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80128	0.303
27DAP/17DAP	1.13863	0.847
39DAP/27DAP	1.13329	0.825
41DAP/39DAP	0.92092	0.697
42DAP/41DAP	1.13276	0.712
43DAP/42DAP	1.38153	0.831
47DAP/43DAP	1.06358	0.825
52DAP/47DAP	1.54279	0.521
57DAP/52DAP	1.14696	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16677	0.994
17DAP/reference	1.30692	0.074
27DAP/reference	0.83445	0.182
39DAP/reference	0.97734	0.75
41DAP/reference	0.95549	0.667
42DAP/reference	1.23107	0.02
43DAP/reference	1.03394	0.812
47DAP/reference	1.17173	0.199
52DAP/reference	1.61294	0.04
57DAP/reference	1.41528	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16514	0.687
27DAP/17DAP	1.33702	0.186
39DAP/27DAP	1.06358	0.728
41DAP/39DAP	1.06176	1
42DAP/41DAP	0.99165	0.83
43DAP/42DAP	1.30507	0.066
47DAP/43DAP	0.8128	0.134
52DAP/47DAP	0.99496	0.9
57DAP/52DAP	1.09061	0.798
57DAP/7DAP	1.32151	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76866	0.057
17DAP/reference	0.85198	0.056
27DAP/reference	0.74409	0.014
39DAP/reference	0.77846	0.043
41DAP/reference	0.68318	0.019
42DAP/reference	0.7096	0.013
43DAP/reference	0.886	0.175
47DAP/reference	1.07489	0.822
52DAP/reference	0.74049	0.015
57DAP/reference	0.688	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74763	0.17
17DAP/reference	1.26935	0.658
27DAP/reference	0.8739	0.292
39DAP/reference	1.36053	0.213
41DAP/reference	1.24396	0.194
42DAP/reference	1.19722	0.054
43DAP/reference	0.93126	0.43
47DAP/reference	0.93261	0.141
52DAP/reference	1.44898	0.528
57DAP/reference	0.70589	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94039	0.249
17DAP/reference	0.90418	0.407
27DAP/reference	0.89382	0.14
39DAP/reference	1.01372	0.693
41DAP/reference	0.87579	0.107
42DAP/reference	1.19586	0.287
43DAP/reference	1.02112	0.827
47DAP/reference	1.01883	0.667
52DAP/reference	0.97885	0.69
57DAP/reference	1.11955	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23175	1
26DAP/20DAP	0.78081	1
34DAP/26DAP	1.21709	1
51DAP/34DAP	0.86856	0.385
52DAP/51DAP	1.03213	1
53DAP/52DAP	1.28642	0.806
55DAP/53DAP	1.06657	0.876
57DAP/55DAP	0.84403	0.548
62DAP/57DAP	0.96699	0.871
68DAP/62DAP	1.32423	0.788
68DAP/14DAP	0.86482	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.39955	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.62321	0.149
Immature Eggplant/Mature Eggplant	6.28377	0.053
Ripe Pepper/Ripe Tomato	1.02232
Mature Eggplant/Ripe Tomato	6.22753	0.268

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	0.80561
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	0.74306
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	N/A	N/A
IL2-6/WTpooled	1.22302
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10325
IL12-4/WTpooled	1.56963	0.516
IL1-4/WTpooled	1.34787	1
WT/WTpooled	0.94543	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	0.98557	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92195	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.57459	0.158

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99142	1
DC3000 delta B/DC3000 delta AB	0.97473	0.849

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14311	1
Exp 36h	0.57045	0.449
Exp 60h	1.1657	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0329	1
Var 0h	0.93047	1
Var 12h I row2-row1	1.01974	1
Var 12h NI row2-row1	1.26959	0.34
Var 36h I row2-row1	1.12895	0.742
Var 36h NI row2-row1	1.16771	1
Var 60h I row2-row1	0.77394	0.582
Var 60h NI row2-row1	0.99852	1
Time course 0hI-0hNI	0.95233	0.758
Time course 12hI-12hNI	0.91137	0.306
Time course 36hI-36hNI	0.79425	0.062
Time course 60hI-60hNI	0.76436	0.047

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)	0.88557	0.529
transgenic ySAMdc/azygous control (breaker)	0.84282	0.49
transgenic ySAMdc/azygous control (red)	0.91891	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08784	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15952	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.38844	0.307
Manapal/WT (break)	1.20447	0.183
Manapal/WT (red)	1.2878	0.413