Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.8.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09382	0.904
27DAP/17DAP	1.29889	0.735
39DAP/27DAP	1.52201	0.199
41DAP/39DAP	1.0482	0.985
42DAP/41DAP	1.44498	0.236
43DAP/42DAP	1.20675	0.724
47DAP/43DAP	2.00773	0.444
52DAP/47DAP	0.79673	0.502
57DAP/52DAP	1.41049	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69512	0.03
17DAP/reference	0.83944	0.046
27DAP/reference	0.83846	0.028
39DAP/reference	1.10659	0.654
41DAP/reference	0.94686	0.542
42DAP/reference	1.2291	0.002
43DAP/reference	2.59222	0.007
47DAP/reference	2.6699	0.001
52DAP/reference	2.18838	0.007
57DAP/reference	1.97911	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06012	0.858
27DAP/17DAP	1.03742	0.887
39DAP/27DAP	1.29861	0.075
41DAP/39DAP	0.9511	0.893
42DAP/41DAP	1.27798	0.023
43DAP/42DAP	1.58424	0.018
47DAP/43DAP	1.34003	0.022
52DAP/47DAP	0.8786	0.452
57DAP/52DAP	0.91873	0.494
57DAP/7DAP	1.61707	0.159

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51967	0.058
17DAP/reference	0.47625	0.011
27DAP/reference	0.69017	0.013
39DAP/reference	0.82731	0.034
41DAP/reference	0.75924	0.026
42DAP/reference	0.84635	0.037
43DAP/reference	0.92213	0.292
47DAP/reference	1.07082	0.717
52DAP/reference	0.83998	0.049
57DAP/reference	0.79788	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55988	0.005
17DAP/reference	0.62021	0.004
27DAP/reference	0.7693	0.123
39DAP/reference	0.80902	0.022
41DAP/reference	1.17167	0.599
42DAP/reference	0.98484	0.594
43DAP/reference	0.77488	0.092
47DAP/reference	0.95481	0.319
52DAP/reference	0.69906	0.004
57DAP/reference	0.80321	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43851	0.031
17DAP/reference	0.73388	0.182
27DAP/reference	0.50552	0.025
39DAP/reference	0.80975	0.05
41DAP/reference	0.69809	0.025
42DAP/reference	1.40427	0.012
43DAP/reference	2.02071	0.016
47DAP/reference	2.66592	0.005
52DAP/reference	3.18036	0.027
57DAP/reference	2.2442	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00505	1
26DAP/20DAP	1.04618	0.886
34DAP/26DAP	1.14123	0.819
51DAP/34DAP	1.47508	0.061
52DAP/51DAP	0.73921	0.151
53DAP/52DAP	2.44122	0.039
55DAP/53DAP	1.05178	0.911
57DAP/55DAP	1.23436	0.626
62DAP/57DAP	0.58758	0.005
68DAP/62DAP	0.85367
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.66694	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.36421	0.073
Mature Green Tomato/Ripe Tomato	0.13851	0.014
Immature Eggplant/Mature Eggplant	1.04813	0.348
Ripe Pepper/Ripe Tomato	0.5387	0.224
Mature Eggplant/Ripe Tomato	0.16271	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10078	0.877
1-1-2/M82	1.16035	1
12-2/M82	0.99873	1
12-4/M82	1.45331	1
1-3/M82	2.15474	0.248
2-1-1/M82	0.92972	0.465
2-1/M82	0.81308	0.322
2-6/M82	1.04485	1
3-2/M82	1.31591	0.549
4-1-1/M82	1.22921	1
4-1/M82	1.32746	1
4-3-2/M82	1.61345	0.284
4-3/M82	0.92557	1
5-3/M82	0.99862	1
6-2/M82	0.29133	0.481
6-3/M82	1.0925	1
7-1/M82	1.06353	0.992
7-2/M82	1.38348	1
9-3-2/M82	1.48501

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.6643	0.71
IL1-4/WTpooled	1.33529
WT/WTpooled	1.06266	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	1.0971	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08162	0.921
DC3000/delta hrp 6h	0.89074	0.95
DC3000/delta hrp 12h	1.09712	1
DC3000/delta hrp 24h	1.03235	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.5624	0.441
DC3000 delta B/DC3000 delta AB	1.16411	0.324

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.51478	0.254
Exp 36h	1.06613	1
Exp 60h	1.34954	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05878	1
Var 0h	0.75979	1
Var 12h I row2-row1	0.96929	0.948
Var 12h NI row2-row1	1.18718	1
Var 36h I row2-row1	1.09283	0.339
Var 36h NI row2-row1	0.67405	0.23
Var 60h I row2-row1	0.93991	0.582
Var 60h NI row2-row1	0.8142	0.292
Time course 0hI-0hNI	0.93599	0.501
Time course 12hI-12hNI	1.01486	0.833
Time course 36hI-36hNI	1.32237	0.114
Time course 60hI-60hNI	1.71471	0.008

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)	0.98907	0.722
transgenic ySAMdc/azygous control (breaker)	0.70184	0.15
transgenic ySAMdc/azygous control (red)	1.11555	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02676	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88837	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97002	1
Manapal/WT (break)	1.15867	0.381
Manapal/WT (red)	0.9187	0.503