Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.11.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16872	0.63
27DAP/17DAP	0.56115	0.074
39DAP/27DAP	0.82738	0.529
41DAP/39DAP	0.72936	0.183
42DAP/41DAP	1.04953	1
43DAP/42DAP	1.03525	1
47DAP/43DAP	0.71035	0.236
52DAP/47DAP	1.73872	0.285
57DAP/52DAP	0.74374	0.727

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68731	0.025
17DAP/reference	0.60497	0.008
27DAP/reference	0.5882	0.016
39DAP/reference	0.62879	0.029
41DAP/reference	0.47923	0.009
42DAP/reference	0.49302	0.001
43DAP/reference	0.45141	0.014
47DAP/reference	0.40578	0.001
52DAP/reference	0.34002	0.012
57DAP/reference	0.40306	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.71242	0.107
27DAP/17DAP	0.65424
39DAP/27DAP	0.40347	0.041
41DAP/39DAP	1.28817	0.029
42DAP/41DAP	0.82409	0.066
43DAP/42DAP	0.70978	0.034
47DAP/43DAP	0.82734	0.28
52DAP/47DAP	0.8553	0.304
57DAP/52DAP	0.84726	0.189
57DAP/7DAP	0.31003	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10697	0.545
17DAP/reference	1.02815	0.971
27DAP/reference	0.77579	0.011
39DAP/reference	0.63842	0.011
41DAP/reference	0.55035	0.011
42DAP/reference	0.51252	0.01
43DAP/reference	0.48856	0.011
47DAP/reference	0.447	0.026
52DAP/reference	0.51525	0.012
57DAP/reference	0.57411	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64618	0.022
17DAP/reference	0.62387	0.012
27DAP/reference	0.70446	0.067
39DAP/reference	0.44832	0.009
41DAP/reference	0.57481	0.007
42DAP/reference	0.52258	0.012
43DAP/reference	0.33643	0.002
47DAP/reference	0.44774	0.007
52DAP/reference	0.32779	0.003
57DAP/reference	0.28537	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.18029	0.015
17DAP/reference	2.10793	0.037
27DAP/reference	1.53241	0.022
39DAP/reference	1.19028	0.466
41DAP/reference	0.8601	0.077
42DAP/reference	0.65197	0.019
43DAP/reference	0.6296	0.026
47DAP/reference	0.35481	0.004
52DAP/reference	0.52588	0.083
57DAP/reference	0.72763	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00794	1
26DAP/20DAP	1.13749	0.813
34DAP/26DAP	0.96151	0.927
51DAP/34DAP	0.52043	0.064
52DAP/51DAP	0.95911	1
53DAP/52DAP	0.54334	0.049
55DAP/53DAP	0.97562	0.807
57DAP/55DAP	1.17028	0.927
62DAP/57DAP	1.13692	0.8
68DAP/62DAP	0.80656	0.095
68DAP/14DAP	0.71349	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.53061	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.92522	0.058
Mature Green Tomato/Ripe Tomato	7.26374	0.015
Immature Eggplant/Mature Eggplant	0.42653	0.062
Ripe Pepper/Ripe Tomato	12.0127	0.236
Mature Eggplant/Ripe Tomato	24.8439	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91013	0.499
1-1-2/M82	0.96472	1
12-2/M82	0.83016	0.955
12-4/M82	1.17967	1
1-3/M82	0.81535	0.378
2-1-1/M82	0.8347
2-1/M82	N/A	N/A
2-6/M82	1.12835	0.425
3-2/M82	0.95366
4-1-1/M82	0.94058	1
4-1/M82	1.13078
4-3-2/M82	1.30607	0.284
4-3/M82	N/A	N/A
5-3/M82	1.10546	1
6-2/M82	1.0275
6-3/M82	1.07192	1
7-1/M82	N/A	N/A
7-2/M82	0.9464	1
9-3-2/M82	1.04888	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21961
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03192	1
IL12-4/WTpooled	1.2874
IL1-4/WTpooled	1.33567
WT/WTpooled	0.98033	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	1.10664	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00396	1
DC3000/delta hrp 6h	0.95602	0.95
DC3000/delta hrp 12h	1.2274	1
DC3000/delta hrp 24h	1.00596

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87281	0.365
DC3000 delta B/DC3000 delta AB	0.49788	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01445	1
Exp 36h	0.77533	0.504
Exp 60h	0.73284	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02398	1
Var 0h	1.01522	1
Var 12h I row2-row1	1.36387	0.795
Var 12h NI row2-row1	0.95067	0.906
Var 36h I row2-row1	0.85029	1
Var 36h NI row2-row1	1.08724	1
Var 60h I row2-row1	1.5117	0.562
Var 60h NI row2-row1	1.01481	1
Time course 0hI-0hNI	0.99844	1
Time course 12hI-12hNI	0.99428	1
Time course 36hI-36hNI	1.046	0.513
Time course 60hI-60hNI	0.2408	0.007

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)	1.09096	0.798
transgenic ySAMdc/azygous control (breaker)	2.49287	0.162
transgenic ySAMdc/azygous control (red)	1.06103	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.62259	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.20045	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	18.7818	0.083
Manapal/WT (break)	6.06967	0.123
Manapal/WT (red)	2.48707	0.413