Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.20.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01261	0.961
27DAP/17DAP	1.26351	0.793
39DAP/27DAP	1.06399	1
41DAP/39DAP	1.15324	0.398
42DAP/41DAP	0.9827	1
43DAP/42DAP	1.06218	1
47DAP/43DAP	0.98192	0.859
52DAP/47DAP	1.53023	0.349
57DAP/52DAP	1.23162	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99329	0.806
17DAP/reference	1.22824	0.653
27DAP/reference	1.11035
39DAP/reference	1.07676
41DAP/reference	1.01281	1
42DAP/reference	0.9626	0.372
43DAP/reference	0.71651
47DAP/reference	1.01842	0.674
52DAP/reference	0.88939	0.405
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01337	0.75
27DAP/17DAP	1.08105	0.798
39DAP/27DAP	0.88956	0.502
41DAP/39DAP	1.11537	0.799
42DAP/41DAP	0.89023	0.486
43DAP/42DAP	1.03924	1
47DAP/43DAP	1.0672	0.88
52DAP/47DAP	1.013	0.991
57DAP/52DAP	1.45249	0.057
57DAP/7DAP	1.57541

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94753	0.203
17DAP/reference	0.84476	0.015
27DAP/reference	0.81565	0.012
39DAP/reference	0.84193	0.027
41DAP/reference	0.78906	0.017
42DAP/reference	0.72459	0.01
43DAP/reference	0.88995	0.016
47DAP/reference	0.78962	0.057
52DAP/reference	0.8606	0.043
57DAP/reference	1.00657	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81117	0.083
17DAP/reference	0.71675	0.07
27DAP/reference	1.05746	0.607
39DAP/reference	0.78001	0.183
41DAP/reference	0.71285
42DAP/reference	0.9334	0.482
43DAP/reference	1.2359	0.144
47DAP/reference	0.96691	0.527
52DAP/reference	0.73123	0.012
57DAP/reference	1.23263	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83838	0.074
17DAP/reference	0.80963	0.056
27DAP/reference	0.79613	0.036
39DAP/reference	0.79907	0.018
41DAP/reference	0.90895	0.107
42DAP/reference	0.85552	0.059
43DAP/reference	0.80566	0.023
47DAP/reference	0.88347	0.168
52DAP/reference	0.80199	0.177
57DAP/reference	1.03267	0.873

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12052	1
26DAP/20DAP	1.48073	0.223
34DAP/26DAP	1.03756	1
51DAP/34DAP	0.85615	0.268
52DAP/51DAP	1.07172	1
53DAP/52DAP	0.72111	0.715
55DAP/53DAP	0.78516	0.135
57DAP/55DAP	0.68541	0.135
62DAP/57DAP	1.17248	0.767
68DAP/62DAP	1.4067	0.767
68DAP/14DAP	1.02578	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27699	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.75816	0.287
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.1592
Mature Eggplant/Ripe Tomato	1.13862	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.06158
12-2/M82	N/A	N/A
12-4/M82	1.15359	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	0.71712
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	1.31926
5-3/M82	0.86786	0.447
6-2/M82	N/A	N/A
6-3/M82	0.73529
7-1/M82	N/A	N/A
7-2/M82	0.81201
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08058	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.95279	1
IL7-3/WTpooled	0.53066
IL12-4/WTpooled	0.94352
IL1-4/WTpooled	0.93626	0.402
WT/WTpooled	1.07001	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	1.18821	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07873	0.921
DC3000/delta hrp 6h	1.92572
DC3000/delta hrp 12h	1.11851	1
DC3000/delta hrp 24h	1.04109	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	15.0838
DC3000 delta B/DC3000 delta AB	0.59979

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89907	1
Exp 36h	1.01969	0.943
Exp 60h	1.11108	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05052	1
Var 0h	N/A	N/A
Var 12h I row2-row1	2.59542	0.406
Var 12h NI row2-row1	1.3543	1
Var 36h I row2-row1	0.94646	0.339
Var 36h NI row2-row1	0.9625	0.852
Var 60h I row2-row1	1.02221	0.562
Var 60h NI row2-row1	0.85408	0.977
Time course 0hI-0hNI	0.90354	0.482
Time course 12hI-12hNI	1.32306	0.024
Time course 36hI-36hNI	1.35977	0.063
Time course 60hI-60hNI	1.57051	0.008

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)	0.94684	0.297
transgenic ySAMdc/azygous control (breaker)	0.89567	0.142
transgenic ySAMdc/azygous control (red)	0.74729	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95637	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9343	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87173	1
Manapal/WT (break)	0.85648	0.333
Manapal/WT (red)	0.7241	0.181