Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.39235	0.014
27DAP/17DAP	0.49005	0.051
39DAP/27DAP	0.95047	0.608
41DAP/39DAP	0.41656	0.041
42DAP/41DAP	0.78795	1
43DAP/42DAP	1.16521	0.976
47DAP/43DAP	0.74686	0.276
52DAP/47DAP	0.92322	0.758
57DAP/52DAP	1.04584	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.11484	0.018
17DAP/reference	1.32026	0.086
27DAP/reference	1.44772	0.008
39DAP/reference	0.5697	0.012
41DAP/reference	0.80963	0.267
42DAP/reference	0.7224	0.01
43DAP/reference	0.79999	0.555
47DAP/reference	0.7704	0.116
52DAP/reference	0.44637	0.01
57DAP/reference	0.61182	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43623	0.03
27DAP/17DAP	1.6008	0.079
39DAP/27DAP	0.59643	0.03
41DAP/39DAP	0.45788	0.013
42DAP/41DAP	0.97494	0.752
43DAP/42DAP	1.28799	0.014
47DAP/43DAP	0.86592	0.069
52DAP/47DAP	1.00574	0.969
57DAP/52DAP	0.92123	0.382
57DAP/7DAP	0.48588	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.66886	0.024
17DAP/reference	1.52845	0.028
27DAP/reference	0.95186	0.348
39DAP/reference	0.71436	0.011
41DAP/reference	0.69172	0.016
42DAP/reference	0.87731	0.169
43DAP/reference	0.76979	0.018
47DAP/reference	0.52465	0.03
52DAP/reference	0.6092	0.011
57DAP/reference	0.74921	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.61281	0.116
17DAP/reference	1.60896	0.066
27DAP/reference	1.2287	0.26
39DAP/reference	0.57617	0.029
41DAP/reference	0.72433	0.014
42DAP/reference	0.92976	0.261
43DAP/reference	0.47902	0.002
47DAP/reference	0.57111	0.008
52DAP/reference	0.46317	0.004
57DAP/reference	0.50469	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.08802	0.015
17DAP/reference	2.32643	0.091
27DAP/reference	2.54454	0.016
39DAP/reference	0.95993	0.464
41DAP/reference	0.8581	0.237
42DAP/reference	0.72003	0.087
43DAP/reference	0.71629	0.064
47DAP/reference	0.35462	0.004
52DAP/reference	0.57055	0.088
57DAP/reference	0.50058	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03754	0.966
26DAP/20DAP	1.34128	0.259
34DAP/26DAP	0.75816	0.138
51DAP/34DAP	0.52913	0.049
52DAP/51DAP	0.97382	1
53DAP/52DAP	0.78325	0.049
55DAP/53DAP	0.60106	0.016
57DAP/55DAP	0.7997	0.178
62DAP/57DAP	1.14926	0.678
68DAP/62DAP	1.32037	0.722
68DAP/14DAP	0.14731	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.22489	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.85952	0.068
Mature Green Tomato/Ripe Tomato	9.50679	0.015
Immature Eggplant/Mature Eggplant	0.3836	0.063
Ripe Pepper/Ripe Tomato	56.7962	0.256
Mature Eggplant/Ripe Tomato	69.1182	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.69177
12-2/M82	N/A	N/A
12-4/M82	0.83843
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	1.31025
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	1.13595

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1571	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.15824
IL7-3/WTpooled	1.37311
IL12-4/WTpooled	1.07007	0.695
IL1-4/WTpooled	1.15389	1
WT/WTpooled	1.00718	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	0.77149	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00444	1
DC3000/delta hrp 6h	1.03264	0.857
DC3000/delta hrp 12h	0.95466	1
DC3000/delta hrp 24h	0.66675	0.17

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53113	0.029
DC3000 delta B/DC3000 delta AB	0.4062	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95107	1
Exp 36h	0.77361	0.449
Exp 60h	0.70883	0.253

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	N/A	N/A
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)	0.74092	0.309
transgenic ySAMdc/azygous control (breaker)	2.44758	1
transgenic ySAMdc/azygous control (red)	0.96061	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.64126	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	5.25744	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.3818	0.105
Manapal/WT (break)	1.91176	1
Manapal/WT (red)	0.99434	0.863