Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62609	0.134
27DAP/17DAP	0.46915	0.031
39DAP/27DAP	1.08111	0.82
41DAP/39DAP	0.56456	0.045
42DAP/41DAP	1.58978	0.709
43DAP/42DAP	1.04583	1
47DAP/43DAP	0.95187	0.799
52DAP/47DAP	0.82803	0.534
57DAP/52DAP	1.18285	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90427	0.085
17DAP/reference	0.99088	0.819
27DAP/reference	0.95653	0.484
39DAP/reference	1.00942	0.828
41DAP/reference	0.96479	0.667
42DAP/reference	0.89319	0.012
43DAP/reference	0.94557	0.5
47DAP/reference	0.91612	0.09
52DAP/reference	1.00119	0.749
57DAP/reference	0.94267	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.35857	0.033
27DAP/17DAP	1.16406	0.471
39DAP/27DAP	0.58421	0.028
41DAP/39DAP	0.56698	0.027
42DAP/41DAP	1.05527	0.81
43DAP/42DAP	1.1375	0.446
47DAP/43DAP	1.26212	0.681
52DAP/47DAP	1.19913	0.449
57DAP/52DAP	1.06981	0.871
57DAP/7DAP	0.294	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93404	0.326
17DAP/reference	1.03149	0.971
27DAP/reference	1.18331	0.015
39DAP/reference	1.21047	0.297
41DAP/reference	0.95662	0.394
42DAP/reference	1.12759	0.308
43DAP/reference	0.99166	0.608
47DAP/reference	0.85089	0.101
52DAP/reference	1.04689	0.941
57DAP/reference	0.95253	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81264	0.157
17DAP/reference	0.70651	0.016
27DAP/reference	0.98376	0.598
39DAP/reference	1.03229	1
41DAP/reference	0.96466	0.412
42DAP/reference	0.9832	0.482
43DAP/reference	0.85356	0.175
47DAP/reference	0.85205	0.044
52DAP/reference	0.87385	0.143
57DAP/reference	0.72471	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01115	0.804
17DAP/reference	0.93496	0.374
27DAP/reference	0.97135	0.539
39DAP/reference	0.95368	0.464
41DAP/reference	0.91066	0.185
42DAP/reference	0.94311	0.445
43DAP/reference	0.89082	0.237
47DAP/reference	0.84529	0.093
52DAP/reference	0.85079	0.15
57DAP/reference	1.01828	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10255	0.966
26DAP/20DAP	1.39752	0.187
34DAP/26DAP	0.98942	1
51DAP/34DAP	0.65343	0.073
52DAP/51DAP	0.80421	0.151
53DAP/52DAP	0.7889
55DAP/53DAP	0.78515	0.43
57DAP/55DAP	0.67891	0.019
62DAP/57DAP	1.74668	0.868
68DAP/62DAP	1.20527	0.729
68DAP/14DAP	1.54316	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15486	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.42559	0.128
Mature Green Tomato/Ripe Tomato	4.52381	0.015
Immature Eggplant/Mature Eggplant	1.09418	0.267
Ripe Pepper/Ripe Tomato	0.78464
Mature Eggplant/Ripe Tomato	0.90007	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03811	0.877
1-1-2/M82	0.83793	0.804
12-2/M82	1.12421	1
12-4/M82	1.23691	0.694
1-3/M82	0.96605	1
2-1-1/M82	1.08553	0.689
2-1/M82	1.39812
2-6/M82	1.11313	0.695
3-2/M82	0.74253	0.455
4-1-1/M82	0.81895	1
4-1/M82	1.1775
4-3-2/M82	0.96992
4-3/M82	0.88249	0.72
5-3/M82	0.99635	1
6-2/M82	0.95464	1
6-3/M82	1.17179	1
7-1/M82	0.697
7-2/M82	1.0708	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31416	0.493
IL2-6/WTpooled	1.02103	1
IL7-5/WTpooled	0.61557
IL7-3/WTpooled	1.01971	1
IL12-4/WTpooled	1.13209	0.839
IL1-4/WTpooled	0.78013
WT/WTpooled	0.93819	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	1.11532	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00599	0.921
DC3000/delta hrp 6h	0.97547	0.95
DC3000/delta hrp 12h	0.95939	1
DC3000/delta hrp 24h	1.05257	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.36901	0.023
DC3000 delta B/DC3000 delta AB	0.39443	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.38869	0.371
Exp 60h	0.91791	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9732	1
Var 0h	0.48827	1
Var 12h I row2-row1	0.7612	0.353
Var 12h NI row2-row1	0.84781	0.488
Var 36h I row2-row1	1.01566	1
Var 36h NI row2-row1	1.13259	1
Var 60h I row2-row1	1.31643	0.543
Var 60h NI row2-row1	1.12899	0.904
Time course 0hI-0hNI	0.97572	0.908
Time course 12hI-12hNI	0.87041	0.132
Time course 36hI-36hNI	0.70729	0.023
Time course 60hI-60hNI	0.08566	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)	1.23235	0.264
transgenic ySAMdc/azygous control (breaker)	1.07323	1
transgenic ySAMdc/azygous control (red)	1.13553	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98147	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22543	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88325	1
Manapal/WT (break)	0.76312	0.333
Manapal/WT (red)	0.83145	0.274