Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.3.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11682	0.812
27DAP/17DAP	0.97515	0.994
39DAP/27DAP	0.87487	0.378
41DAP/39DAP	1.02264	0.964
42DAP/41DAP	1.03761	0.971
43DAP/42DAP	1.00695	1
47DAP/43DAP	0.97378	0.89
52DAP/47DAP	0.99249	0.967
57DAP/52DAP	0.91846	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90851	0.455
17DAP/reference	N/A	N/A
27DAP/reference	N/A	N/A
39DAP/reference	N/A	N/A
41DAP/reference	0.54632
42DAP/reference	0.99584	0.608
43DAP/reference	N/A	N/A
47DAP/reference	1.05915	0.495
52DAP/reference	0.9286
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99291	0.826
27DAP/17DAP	1.12914	0.621
39DAP/27DAP	0.95935	0.529
41DAP/39DAP	0.99783	1
42DAP/41DAP	1.01296	0.976
43DAP/42DAP	1.01917	0.478
47DAP/43DAP	1.00002	1
52DAP/47DAP	1.0028	1
57DAP/52DAP	0.96646	0.494
57DAP/7DAP	0.95383	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87489	0.183
17DAP/reference	0.73524	0.013
27DAP/reference	0.73969	0.022
39DAP/reference	0.85091	0.016
41DAP/reference	0.84449	0.012
42DAP/reference	0.71612	0.01
43DAP/reference	0.69292	0.011
47DAP/reference	0.80359	0.079
52DAP/reference	0.70157	0.026
57DAP/reference	0.74136	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98188	0.811
17DAP/reference	0.95042	0.487
27DAP/reference	0.93026
39DAP/reference	0.92506	0.168
41DAP/reference	0.94393	0.194
42DAP/reference	1.02566	0.794
43DAP/reference	0.91293	0.378
47DAP/reference	1.02855	0.513
52DAP/reference	0.93556	0.043
57DAP/reference	0.87453	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8939	0.169
17DAP/reference	0.99821	0.855
27DAP/reference	0.78087	0.065
39DAP/reference	0.71602	0.015
41DAP/reference	0.85095	0.086
42DAP/reference	0.70881	0.071
43DAP/reference	0.79407	0.054
47DAP/reference	0.94616	0.269
52DAP/reference	0.6052	0.072
57DAP/reference	0.85699	0.273

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0026	1
26DAP/20DAP	1.10627	0.66
34DAP/26DAP	1.02065	1
51DAP/34DAP	1.01275	0.962
52DAP/51DAP	0.92145	1
53DAP/52DAP	1.01543	0.961
55DAP/53DAP	0.92981	0.648
57DAP/55DAP	0.99669	0.944
62DAP/57DAP	1.12296	0.445
68DAP/62DAP	1.18202	0.8
68DAP/14DAP	1.13514	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94997	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27445	0.089
Mature Green Tomato/Ripe Tomato	1.22883	0.267
Immature Eggplant/Mature Eggplant	1.05243	1
Ripe Pepper/Ripe Tomato	2.41958	0.258
Mature Eggplant/Ripe Tomato	1.86001	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97887	0.961
1-1-2/M82	1.00169	1
12-2/M82	0.92532	0.955
12-4/M82	1.0296	1
1-3/M82	0.97514	0.441
2-1-1/M82	1.03005	1
2-1/M82	1.2652	1
2-6/M82	0.93733	1
3-2/M82	0.98564	1
4-1-1/M82	0.9812	1
4-1/M82	0.99742	1
4-3-2/M82	0.99875	1
4-3/M82	0.87028	0.72
5-3/M82	1.01522	0.378
6-2/M82	1.00068	1
6-3/M82	1.00883	1
7-1/M82	1.00606	1
7-2/M82	0.97905	0.881
9-3-2/M82	0.85397	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.06713	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87523	1
IL12-4/WTpooled	0.95044	1
IL1-4/WTpooled	0.92663	0.562
WT/WTpooled	1.07316	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	1.10862	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02809	0.921
DC3000/delta hrp 6h	1.04629
DC3000/delta hrp 12h	0.80772	1
DC3000/delta hrp 24h	0.91895	0.363

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8449	0.057
DC3000 delta B/DC3000 delta AB	0.84096	0.033

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98067	1
Exp 36h	0.77432	0.449
Exp 60h	0.76166	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0406	1
Var 0h	1.17293	1
Var 12h I row2-row1	1.22577	0.283
Var 12h NI row2-row1	0.96408	0.906
Var 36h I row2-row1	1.2816	0.309
Var 36h NI row2-row1	1.0674	1
Var 60h I row2-row1	0.8367	0.292
Var 60h NI row2-row1	0.95849	1
Time course 0hI-0hNI	1.0313	0.867
Time course 12hI-12hNI	1.04232	0.743
Time course 36hI-36hNI	1.13104	0.248
Time course 60hI-60hNI	1.39082	0.426

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)	0.89263	0.338
transgenic ySAMdc/azygous control (breaker)	1.67642	0.248
transgenic ySAMdc/azygous control (red)	1.18637	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90555	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.3839	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.7266	0.083
Manapal/WT (break)	1.80232	0.14
Manapal/WT (red)	0.96612	0.728