Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31035	0.219
27DAP/17DAP	1.18632	0.833
39DAP/27DAP	1.0304	1
41DAP/39DAP	0.82451	0.385
42DAP/41DAP	1.01124	1
43DAP/42DAP	1.06728	1
47DAP/43DAP	1.21789	0.576
52DAP/47DAP	2.47043	0.61
57DAP/52DAP	1.14166	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67313	0.024
17DAP/reference	0.66188	0.079
27DAP/reference	1.1178	0.184
39DAP/reference	0.75598	0.011
41DAP/reference	0.644	0.012
42DAP/reference	0.95551	0.384
43DAP/reference	0.57848	0.031
47DAP/reference	0.73776	0.008
52DAP/reference	0.56802	0.012
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16565	0.241
27DAP/17DAP	0.96141	0.821
39DAP/27DAP	0.84989	0.256
41DAP/39DAP	1.10662	0.663
42DAP/41DAP	0.97709	0.776
43DAP/42DAP	0.92475	0.246
47DAP/43DAP	0.97102	0.902
52DAP/47DAP	1.16935	0.498
57DAP/52DAP	1.18875	0.293
57DAP/7DAP	0.91969	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18531	0.218
17DAP/reference	0.82623	0.064
27DAP/reference	0.59137	0.01
39DAP/reference	0.49118	0.012
41DAP/reference	0.39999	0.011
42DAP/reference	0.30577	0.01
43DAP/reference	0.27874	0.009
47DAP/reference	0.54093	0.168
52DAP/reference	0.32296	0.01
57DAP/reference	0.37032	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60227	0.008
17DAP/reference	0.83923	0.201
27DAP/reference	1.20039	0.607
39DAP/reference	0.98271	0.554
41DAP/reference	0.9817	0.493
42DAP/reference	0.92902	0.237
43DAP/reference	0.58479	0.017
47DAP/reference	0.7806	0.029
52DAP/reference	0.95067	0.302
57DAP/reference	0.60727	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.53635	0.016
17DAP/reference	1.63587	0.07
27DAP/reference	1.72801	0.02
39DAP/reference	1.25903	0.169
41DAP/reference	0.81474	0.096
42DAP/reference	0.68871	0.087
43DAP/reference	0.89469	0.281
47DAP/reference	1.14853	0.901
52DAP/reference	0.49323	0.066
57DAP/reference	3.86755	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00239	1
26DAP/20DAP	0.82137	0.512
34DAP/26DAP	1.06318	1
51DAP/34DAP	0.78107	0.209
52DAP/51DAP	1.55921	0.051
53DAP/52DAP	0.89344	0.35
55DAP/53DAP	1.26844	0.075
57DAP/55DAP	0.6903	0.101
62DAP/57DAP	1.26798	0.069
68DAP/62DAP	1.81739	0.126
68DAP/14DAP	1.52726	0.084

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59692	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.32354	0.058
Mature Green Tomato/Ripe Tomato	2.74512	0.134
Immature Eggplant/Mature Eggplant	0.51477	0.062
Ripe Pepper/Ripe Tomato	1.29738	0.258
Mature Eggplant/Ripe Tomato	5.8511	0.26

Experiment: IL carotenoid

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

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95117	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.87569	1
IL7-3/WTpooled	1.05528
IL12-4/WTpooled	0.6948	0.554
IL1-4/WTpooled	1.05454	1
WT/WTpooled	1.10024	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	1.10656	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87269	0.941
DC3000/delta hrp 6h	1.01329	1
DC3000/delta hrp 12h	1.61245	1
DC3000/delta hrp 24h	0.58837	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.59107	0.025
DC3000 delta B/DC3000 delta AB	0.55903	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94606	1
Exp 36h	0.85312	0.426
Exp 60h	0.6937	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0049	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.85757
Var 12h NI row2-row1	0.90039
Var 36h I row2-row1	0.99836	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	0.9576	0.821
Time course 12hI-12hNI	0.98196	0.914
Time course 36hI-36hNI	0.90223	0.166
Time course 60hI-60hNI	0.18118	0.005

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)	0.97371	0.662
transgenic ySAMdc/azygous control (breaker)	1.50196	0.248
transgenic ySAMdc/azygous control (red)	1.07835	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.62302	0.104

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.93655	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.95028	0.083
Manapal/WT (break)	3.90675	0.123
Manapal/WT (red)	2.2901	0.413