Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.51731	0.022
27DAP/17DAP	0.57597	0.04
39DAP/27DAP	1.02805	0.82
41DAP/39DAP	0.45849	0.041
42DAP/41DAP	0.91568	1
43DAP/42DAP	1.12862	1
47DAP/43DAP	0.85199	0.54
52DAP/47DAP	1.05202	0.98
57DAP/52DAP	0.99806	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.048	0.006
17DAP/reference	2.12364	0.012
27DAP/reference	2.31966	0.009
39DAP/reference	0.64062	0.033
41DAP/reference	0.60079	0.014
42DAP/reference	0.8565	0.04
43DAP/reference	0.53771	0.015
47DAP/reference	0.53612	0.001
52DAP/reference	0.55769	0.013
57DAP/reference	0.62641	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.50746	0.033
27DAP/17DAP	1.40335	0.196
39DAP/27DAP	0.7353	0.207
41DAP/39DAP	0.63197	0.09
42DAP/41DAP	1.00019	0.87
43DAP/42DAP	0.89048	0.293
47DAP/43DAP	0.82477	0.039
52DAP/47DAP	1.16324	0.616
57DAP/52DAP	1.20781	0.186
57DAP/7DAP	0.47611

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.66628	0.024
17DAP/reference	1.63856	0.014
27DAP/reference	0.95086	0.325
39DAP/reference	0.5217	0.012
41DAP/reference	0.44604	0.01
42DAP/reference	0.74797	0.082
43DAP/reference	0.5624	0.013
47DAP/reference	0.60547	0.101
52DAP/reference	0.54751	0.017
57DAP/reference	0.53441	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96827	0.065
17DAP/reference	2.17876	0.007
27DAP/reference	1.63641	0.052
39DAP/reference	0.81584	0.156
41DAP/reference	1.26403	0.277
42DAP/reference	1.19116	0.302
43DAP/reference	0.46629	0.004
47DAP/reference	0.63898	0.016
52DAP/reference	0.60503	0.01
57DAP/reference	0.49538	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.80052	0.015
17DAP/reference	2.35981	0.013
27DAP/reference	2.72644	0.014
39DAP/reference	1.03188	0.693
41DAP/reference	0.91383	0.417
42DAP/reference	0.70257	0.087
43DAP/reference	0.65164	0.033
47DAP/reference	0.64042	0.054
52DAP/reference	0.56179	0.1
57DAP/reference	1.10583	0.786

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14074	1
26DAP/20DAP	1.10994	0.707
34DAP/26DAP	0.91607	0.783
51DAP/34DAP	0.57431	0.049
52DAP/51DAP	0.99123	1
53DAP/52DAP	0.81433	0.207
55DAP/53DAP	0.53127	0.023
57DAP/55DAP	0.92456	0.731
62DAP/57DAP	0.51959
68DAP/62DAP	0.94472	0.769
68DAP/14DAP	0.19003	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.34364	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.91891	0.063
Mature Green Tomato/Ripe Tomato	2.95967	0.017
Immature Eggplant/Mature Eggplant	0.4402	0.057
Ripe Pepper/Ripe Tomato	39.2289	0.251
Mature Eggplant/Ripe Tomato	52.5509	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83177
12-2/M82	N/A	N/A
12-4/M82	0.96535
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	0.91467
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.31854
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04066	0.493
IL2-6/WTpooled	1.11824	0.427
IL7-5/WTpooled	0.88196	1
IL7-3/WTpooled	1.00341	1
IL12-4/WTpooled	1.03111	0.557
IL1-4/WTpooled	1.09379	1
WT/WTpooled	1.01733	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	0.92801	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0162	1
DC3000/delta hrp 6h	0.9968	0.95
DC3000/delta hrp 12h	1.35383	1
DC3000/delta hrp 24h	0.70721	0.124

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.59068	0.024
DC3000 delta B/DC3000 delta AB	0.5918	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94126	1
Exp 36h	0.83971	0.539
Exp 60h	0.81385	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0253	1
Var 0h	0.808	1
Var 12h I row2-row1	0.9204	0.565
Var 12h NI row2-row1	0.91782	0.627
Var 36h I row2-row1	1.09489	0.291
Var 36h NI row2-row1	1.09556	1
Var 60h I row2-row1	1.00391	1
Var 60h NI row2-row1	0.97112	1
Time course 0hI-0hNI	1.05557	0.574
Time course 12hI-12hNI	0.96633	0.739
Time course 36hI-36hNI	0.96554	0.295
Time course 60hI-60hNI	0.41548	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)	0.74424	0.338
transgenic ySAMdc/azygous control (breaker)	3.84782	0.248
transgenic ySAMdc/azygous control (red)	0.98042	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.55726	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.24151	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15184	0.084
Manapal/WT (break)	1.86102	1
Manapal/WT (red)	1.55598	1