Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87111	0.31
27DAP/17DAP	1.04705	0.881
39DAP/27DAP	1.5206	0.132
41DAP/39DAP	0.91376	0.518
42DAP/41DAP	1.03146	1
43DAP/42DAP	0.9613	0.833
47DAP/43DAP	0.7325	0.245
52DAP/47DAP	1.11035	0.989
57DAP/52DAP	1.07541	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25137	0.101
17DAP/reference	1.05674	0.696
27DAP/reference	1.03692	0.909
39DAP/reference	1.21631	0.262
41DAP/reference	1.09713	0.265
42DAP/reference	1.58053	0.001
43DAP/reference	1.4387	0.008
47DAP/reference	1.9274	0.001
52DAP/reference	1.35264	0.014
57DAP/reference	1.77402	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71886	0.062
27DAP/17DAP	1.31247	0.075
39DAP/27DAP	0.8226	0.059
41DAP/39DAP	0.98918	0.997
42DAP/41DAP	1.08732	0.663
43DAP/42DAP	1.08844	0.513
47DAP/43DAP	0.91498	0.506
52DAP/47DAP	1.01875	0.965
57DAP/52DAP	1.09342	0.601
57DAP/7DAP	0.86042	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.90009	0.033
17DAP/reference	1.64582	0.007
27DAP/reference	1.68399	0.012
39DAP/reference	1.77261	0.005
41DAP/reference	2.14965	0.009
42DAP/reference	1.97053	0.007
43DAP/reference	1.85263	0.006
47DAP/reference	1.79098	0.014
52DAP/reference	2.03544	0.007
57DAP/reference	1.79887	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91015	0.441
17DAP/reference	1.2048	0.338
27DAP/reference	1.49351	0.118
39DAP/reference	1.42772	0.047
41DAP/reference	1.27688	0.166
42DAP/reference	1.69737	0.008
43DAP/reference	0.88113	0.186
47DAP/reference	1.58964	0.008
52DAP/reference	1.04549	1
57DAP/reference	0.74064	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3106	0.041
17DAP/reference	1.08178	0.689
27DAP/reference	1.32392	0.023
39DAP/reference	1.46586	0.008
41DAP/reference	1.32609	0.019
42DAP/reference	1.39796	0.01
43DAP/reference	1.76805	0.03
47DAP/reference	1.27966	0.042
52DAP/reference	1.16141	0.335
57DAP/reference	1.97428	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20009	0.966
26DAP/20DAP	1.71911	0.099
34DAP/26DAP	0.91092	0.666
51DAP/34DAP	1.21162	0.192
52DAP/51DAP	0.7958	0.151
53DAP/52DAP	1.05055	0.921
55DAP/53DAP	0.71473	0.021
57DAP/55DAP	1.03451	0.961
62DAP/57DAP	0.70935	0.28
68DAP/62DAP	1.06689	0.931
68DAP/14DAP	1.82871	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68946	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9622	0.658
Mature Green Tomato/Ripe Tomato	1.05881	0.948
Immature Eggplant/Mature Eggplant	1.17763	0.101
Ripe Pepper/Ripe Tomato	2.17579	0.256
Mature Eggplant/Ripe Tomato	1.13239	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96035	0.944
1-1-2/M82	1.1354	0.977
12-2/M82	1.08064	1
12-4/M82	1.23771	1
1-3/M82	1.63945	0.248
2-1-1/M82	1.01578	1
2-1/M82	0.95374	1
2-6/M82	0.92556	1
3-2/M82	1.03785	0.967
4-1-1/M82	0.88188	1
4-1/M82	1.64203	0.466
4-3-2/M82	1.20193	0.284
4-3/M82	1.2827	0.268
5-3/M82	0.99338	1
6-2/M82	0.89722
6-3/M82	0.90013
7-1/M82	0.96913	1
7-2/M82	1.02133	1
9-3-2/M82	1.20291	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8971	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.6729	0.294
IL12-4/WTpooled	0.98259	1
IL1-4/WTpooled	0.93259
WT/WTpooled	1.03518	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	1.08221	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02937	0.921
DC3000/delta hrp 6h	0.89769	0.95
DC3000/delta hrp 12h	0.9698	1
DC3000/delta hrp 24h	1.00617	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08333	0.384
DC3000 delta B/DC3000 delta AB	1.20265	0.192

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13994	0.254
Exp 36h	1.38477	0.489
Exp 60h	1.26913	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.98723	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
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	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.13693	0.318
transgenic ySAMdc/azygous control (breaker)	0.88366	0.173
transgenic ySAMdc/azygous control (red)	0.98872	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.26315	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55539	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83485	1
Manapal/WT (break)	0.98336	1
Manapal/WT (red)	0.81857	0.315