Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.15.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.62548	0.037
27DAP/17DAP	0.73128	0.184
39DAP/27DAP	0.7558	0.425
41DAP/39DAP	0.8588	0.459
42DAP/41DAP	0.9229	1
43DAP/42DAP	0.94717	0.877
47DAP/43DAP	1.64211	0.201
52DAP/47DAP	1.72322	0.147
57DAP/52DAP	0.80633	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21292	0.049
17DAP/reference	1.08344	0.061
27DAP/reference	1.06523	0.75
39DAP/reference	0.99101	0.841
41DAP/reference	1.22888	0.03
42DAP/reference	1.09706	0.027
43DAP/reference	0.92061	0.36
47DAP/reference	1.08748	0.264
52DAP/reference	1.11566	0.302
57DAP/reference	0.80898	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95482	0.56
27DAP/17DAP	1.07816	0.928
39DAP/27DAP	0.79558	0.322
41DAP/39DAP	0.98841	1
42DAP/41DAP	1.03903	1
43DAP/42DAP	0.94049	0.558
47DAP/43DAP	0.8628	0.192
52DAP/47DAP	0.91078	0.763
57DAP/52DAP	1.19436	0.431
57DAP/7DAP	1.01675	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78391	0.104
17DAP/reference	0.78936	0.056
27DAP/reference	0.80965	0.016
39DAP/reference	0.75005	0.023
41DAP/reference	0.7665	0.012
42DAP/reference	0.61857	0.01
43DAP/reference	0.68402	0.013
47DAP/reference	0.72062	0.101
52DAP/reference	0.6156	0.017
57DAP/reference	0.64958	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2336	0.134
17DAP/reference	1.43741	0.007
27DAP/reference	1.32406	0.038
39DAP/reference	1.17189	0.281
41DAP/reference	1.13157	0.657
42DAP/reference	1.18254	0.059
43DAP/reference	1.06934	0.59
47DAP/reference	1.15839	0.12
52DAP/reference	1.16272	0.043
57DAP/reference	1.32174	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99729	0.699
17DAP/reference	1.12259	0.488
27DAP/reference	0.82123	0.045
39DAP/reference	0.75674	0.024
41DAP/reference	0.80521	0.046
42DAP/reference	0.80685	0.025
43DAP/reference	0.87634	0.179
47DAP/reference	0.86274	0.207
52DAP/reference	0.74481	0.082
57DAP/reference	0.70412	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.10793	0.034
26DAP/20DAP	1.32326	0.322
34DAP/26DAP	1.02285	1
51DAP/34DAP	0.9751	0.863
52DAP/51DAP	1.22681	0.704
53DAP/52DAP	0.77669	0.075
55DAP/53DAP	0.92404	0.698
57DAP/55DAP	1.00615	0.904
62DAP/57DAP	1.14653	0.8
68DAP/62DAP	0.87288	0.769
68DAP/14DAP	0.50961	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7627	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.22422	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	1.08329
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	N/A	N/A
IL2-6/WTpooled	0.94543	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03369	1
IL12-4/WTpooled	0.87351	0.566
IL1-4/WTpooled	0.73198
WT/WTpooled	0.99655	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	0.91862	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.23409	1
DC3000/delta hrp 12h	1.06222	1
DC3000/delta hrp 24h	1.50154	0.046

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73123	0.023
DC3000 delta B/DC3000 delta AB	0.76151	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09164	1
Exp 36h	0.6696	0.539
Exp 60h	0.58545	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00816	1
Var 0h	1.21126	0.936
Var 12h I row2-row1	0.85171	0.467
Var 12h NI row2-row1	1.00272	1
Var 36h I row2-row1	0.96247	1
Var 36h NI row2-row1	1.06964	1
Var 60h I row2-row1	1.61363	0.562
Var 60h NI row2-row1	1.07738	0.701
Time course 0hI-0hNI	1.00548	1
Time course 12hI-12hNI	1.01691	0.861
Time course 36hI-36hNI	0.8283	0.039
Time course 60hI-60hNI	0.28639	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.07495	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84557	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.88141	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.46179	0.083
Manapal/WT (break)	1.53284	0.183
Manapal/WT (red)	N/A	N/A