Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20344	0.646
27DAP/17DAP	0.52403	0.032
39DAP/27DAP	0.83698	0.549
41DAP/39DAP	0.77133	0.245
42DAP/41DAP	0.99396	1
43DAP/42DAP	0.9832	0.931
47DAP/43DAP	0.87877	0.576
52DAP/47DAP	1.81377	0.191
57DAP/52DAP	0.88078	0.765

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90987	0.293
17DAP/reference	0.82283	0.008
27DAP/reference	0.71187	0.012
39DAP/reference	0.69113	0.011
41DAP/reference	0.67963	0.01
42DAP/reference	0.67445	0.001
43DAP/reference	0.65054	0.014
47DAP/reference	0.60858	0.001
52DAP/reference	0.55837	0.012
57DAP/reference	0.60432	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36843	0.051
27DAP/17DAP	0.86675	0.241
39DAP/27DAP	0.69779	0.036
41DAP/39DAP	1.14898	0.266
42DAP/41DAP	1.02411	0.893
43DAP/42DAP	0.88754	0.07
47DAP/43DAP	0.9754	0.886
52DAP/47DAP	0.95613	0.839
57DAP/52DAP	1.04816	0.783
57DAP/7DAP	0.84275	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98846	0.55
17DAP/reference	0.86102	0.011
27DAP/reference	0.78604	0.01
39DAP/reference	0.69829	0.011
41DAP/reference	0.64445	0.012
42DAP/reference	0.72421	0.022
43DAP/reference	0.65204	0.013
47DAP/reference	0.49263	0.038
52DAP/reference	0.63188	0.013
57DAP/reference	0.63091	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66009	0.007
17DAP/reference	0.7055	0.023
27DAP/reference	0.72524	0.016
39DAP/reference	0.53262	0.011
41DAP/reference	0.67325	0.011
42DAP/reference	0.72302	0.02
43DAP/reference	0.57558	0.004
47DAP/reference	0.72915	0.041
52DAP/reference	0.43646	0.003
57DAP/reference	0.44019	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52051	0.016
17DAP/reference	1.56848	0.091
27DAP/reference	1.18534	0.062
39DAP/reference	1.04324	0.496
41DAP/reference	0.81532	0.019
42DAP/reference	0.77079	0.016
43DAP/reference	0.70222	0.019
47DAP/reference	0.58282	0.004
52DAP/reference	0.62134	0.074
57DAP/reference	1.18676	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92572	1
26DAP/20DAP	1.09228	0.806
34DAP/26DAP	0.81199	0.103
51DAP/34DAP	0.60658	0.065
52DAP/51DAP	1.11398	0.367
53DAP/52DAP	0.85477	0.221
55DAP/53DAP	0.98822	0.876
57DAP/55DAP	0.97864	0.911
62DAP/57DAP	1.29448	0.081
68DAP/62DAP	0.86914	0.722
68DAP/14DAP	0.66831	0.064

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92521	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.70272	0.058
Mature Green Tomato/Ripe Tomato	10.2208	0.015
Immature Eggplant/Mature Eggplant	0.50862	0.057
Ripe Pepper/Ripe Tomato	20.2102	1
Mature Eggplant/Ripe Tomato	32.4147	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06584	0.574
1-1-2/M82	N/A	N/A
12-2/M82	0.84537
12-4/M82	1.72242	1
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	0.94954	1
3-2/M82	1.20121
4-1-1/M82	1.02042
4-1/M82	1.0459
4-3-2/M82	1.06446
4-3/M82	1.01025
5-3/M82	1.14386	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.75925
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	1.01441	1
IL2-6/WTpooled	1.06406	0.441
IL7-5/WTpooled	0.92922	1
IL7-3/WTpooled	0.88108	0.293
IL12-4/WTpooled	1.03802	0.839
IL1-4/WTpooled	0.94532	0.562
WT/WTpooled	1.02736	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	1.03385	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8884	0.62
DC3000/delta hrp 6h	0.8244	0.95
DC3000/delta hrp 12h	1.04928	1
DC3000/delta hrp 24h	0.97843	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84733	0.04
DC3000 delta B/DC3000 delta AB	0.58235	0.041

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03274	1
Exp 36h	0.97975	0.943
Exp 60h	0.89437	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03995	1
Var 0h	0.93857	1
Var 12h I row2-row1	1.01179	1
Var 12h NI row2-row1	0.97082	0.906
Var 36h I row2-row1	0.97786	1
Var 36h NI row2-row1	0.91468	0.61
Var 60h I row2-row1	1.44989	0.562
Var 60h NI row2-row1	1.02481	1
Time course 0hI-0hNI	1.05527	0.852
Time course 12hI-12hNI	1.07375	0.738
Time course 36hI-36hNI	1.11382	0.248
Time course 60hI-60hNI	0.60195	0.015

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)	1.09371	0.921
transgenic ySAMdc/azygous control (breaker)	4.23832	0.162
transgenic ySAMdc/azygous control (red)	1.43947	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.69807	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08869	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	29.7297	0.084
Manapal/WT (break)	12.6358	0.123
Manapal/WT (red)	3.08058	0.413