Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.44692	0.018
27DAP/17DAP	0.49948	0.056
39DAP/27DAP	1.08204	0.857
41DAP/39DAP	0.47932	0.041
42DAP/41DAP	1.00289	1
43DAP/42DAP	1.16629	0.869
47DAP/43DAP	0.9422	0.736
52DAP/47DAP	0.73855	0.362
57DAP/52DAP	0.98541	0.976

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.01222	0.01
17DAP/reference	1.36879	0.012
27DAP/reference	1.40209	0.021
39DAP/reference	0.47527	0.007
41DAP/reference	0.55872	0.011
42DAP/reference	0.71105	0.001
43DAP/reference	0.44104	0.014
47DAP/reference	0.58332	0.002
52DAP/reference	0.5491	0.012
57DAP/reference	1.3583	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37613	0.03
27DAP/17DAP	2.33994	0.032
39DAP/27DAP	0.51581	0.033
41DAP/39DAP	0.30001	0.013
42DAP/41DAP	0.96436	0.721
43DAP/42DAP	1.37234	0.015
47DAP/43DAP	0.80858	0.068
52DAP/47DAP	0.99123	0.947
57DAP/52DAP	1.02887	1
57DAP/7DAP	0.24215	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.35398	0.024
17DAP/reference	1.67499	0.011
27DAP/reference	1.06617	0.804
39DAP/reference	0.75887	0.014
41DAP/reference	0.67393	0.016
42DAP/reference	0.98061	0.482
43DAP/reference	0.76165	0.03
47DAP/reference	0.59553	0.035
52DAP/reference	0.64783	0.012
57DAP/reference	0.72179	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42143	0.438
17DAP/reference	1.01423	0.805
27DAP/reference	1.15501	0.352
39DAP/reference	0.74689	0.178
41DAP/reference	0.778	0.032
42DAP/reference	0.91862	0.261
43DAP/reference	0.35426	0.002
47DAP/reference	0.57317	0.007
52DAP/reference	0.81779	0.143
57DAP/reference	0.48068	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	6.38673	0.017
17DAP/reference	2.21465	0.148
27DAP/reference	2.51995	0.013
39DAP/reference	1.12046	0.752
41DAP/reference	0.90937	0.264
42DAP/reference	2.23991	0.199
43DAP/reference	1.07677	0.738
47DAP/reference	0.48711	0.005
52DAP/reference	1.22268	0.8
57DAP/reference	0.92854	0.366

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11841	1
26DAP/20DAP	1.12626	0.7
34DAP/26DAP	0.70109	0.132
51DAP/34DAP	0.53062	0.049
52DAP/51DAP	1.06899	0.534
53DAP/52DAP	0.73151	0.049
55DAP/53DAP	0.50976	0.017
57DAP/55DAP	0.64323	0.029
62DAP/57DAP	1.66606	0.833
68DAP/62DAP	1.09234	1
68DAP/14DAP	0.31822	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.09293	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.18266	0.058
Mature Green Tomato/Ripe Tomato	16.9482	0.015
Immature Eggplant/Mature Eggplant	0.37407	0.062
Ripe Pepper/Ripe Tomato	39.2559	0.236
Mature Eggplant/Ripe Tomato	32.2887	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12311	0.877
1-1-2/M82	1.24414
12-2/M82	N/A	N/A
12-4/M82	0.94666	1
1-3/M82	0.71404
2-1-1/M82	0.65279
2-1/M82	N/A	N/A
2-6/M82	1.04434	0.695
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.0838
4-3-2/M82	N/A	N/A
4-3/M82	0.6322
5-3/M82	1.14364	1
6-2/M82	1.25086
6-3/M82	1.41919
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	0.4081	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.00689	1
IL7-3/WTpooled	2.72684
IL12-4/WTpooled	0.95167	1
IL1-4/WTpooled	0.95363	1
WT/WTpooled	1.04949	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	0.80058	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95208	1
DC3000/delta hrp 6h	0.9127	0.95
DC3000/delta hrp 12h	1.22725	1
DC3000/delta hrp 24h	0.58862	0.121

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62958	0.038
DC3000 delta B/DC3000 delta AB	0.4852	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98722	1
Exp 36h	0.87715	0.471
Exp 60h	0.78076	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99528	1
Var 0h	1.02711	1
Var 12h I row2-row1	0.45073
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.97642	1
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	1.0309	0.852
Time course 12hI-12hNI	0.96582	0.637
Time course 36hI-36hNI	0.89941	0.187
Time course 60hI-60hNI	0.6318	0.006

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)	0.75142	0.32
transgenic ySAMdc/azygous control (breaker)	2.22753	1
transgenic ySAMdc/azygous control (red)	1.03077	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.57381	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.97915	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20491	1
Manapal/WT (break)	2.20287	1
Manapal/WT (red)	1.57096	0.222