Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85711	0.339
27DAP/17DAP	0.83646	0.572
39DAP/27DAP	0.85313	0.583
41DAP/39DAP	0.93416	0.701
42DAP/41DAP	1.57592	0.089
43DAP/42DAP	1.38251	0.409
47DAP/43DAP	0.92229	0.71
52DAP/47DAP	0.98739	0.92
57DAP/52DAP	0.88926	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7894	0.048
17DAP/reference	0.88312	0.041
27DAP/reference	0.94562	0.417
39DAP/reference	0.9047	0.081
41DAP/reference	0.80738	0.065
42DAP/reference	0.84935	0.021
43DAP/reference	0.9367	0.448
47DAP/reference	0.99147	0.568
52DAP/reference	1.11094	0.149
57DAP/reference	1.19337	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92352	0.454
27DAP/17DAP	1.12811	0.569
39DAP/27DAP	0.89193	0.405
41DAP/39DAP	1.27312	0.455
42DAP/41DAP	0.94691	0.607
43DAP/42DAP	0.88936	0.351
47DAP/43DAP	1.05983	0.884
52DAP/47DAP	0.85752	0.702
57DAP/52DAP	1.08545	0.657
57DAP/7DAP	1.48931	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43033	0.037
17DAP/reference	1.64218	0.007
27DAP/reference	1.06283	0.804
39DAP/reference	1.40996	0.114
41DAP/reference	1.48265	0.023
42DAP/reference	1.50183	0.046
43DAP/reference	1.45793	0.034
47DAP/reference	1.31031	0.035
52DAP/reference	1.41706	0.009
57DAP/reference	1.53685	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7655	0.022
17DAP/reference	0.72189	0.037
27DAP/reference	0.87058	0.16
39DAP/reference	0.98195	0.569
41DAP/reference	1.00569	0.749
42DAP/reference	0.95159	0.355
43DAP/reference	0.68866	0.004
47DAP/reference	0.86667	0.102
52DAP/reference	0.91172	0.101
57DAP/reference	0.83962	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20292	0.158
17DAP/reference	1.28608	0.595
27DAP/reference	1.2589	0.164
39DAP/reference	1.16876	0.711
41DAP/reference	1.21657	0.296
42DAP/reference	1.29206	0.194
43DAP/reference	1.32547	0.154
47DAP/reference	1.02795	1
52DAP/reference	1.04512	0.928
57DAP/reference	1.41154	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07558	0.966
26DAP/20DAP	1.41017	0.353
34DAP/26DAP	1.19945	1
51DAP/34DAP	1.40116	0.96
52DAP/51DAP	0.65564	0.151
53DAP/52DAP	0.76347
55DAP/53DAP	0.93658	0.775
57DAP/55DAP	1.09994	0.97
62DAP/57DAP	2.05616	0.303
68DAP/62DAP	1.69528	0.153
68DAP/14DAP	2.10483	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.38872	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9138
Mature Green Tomato/Ripe Tomato	1.19981	0.69
Immature Eggplant/Mature Eggplant	0.67859	0.064
Ripe Pepper/Ripe Tomato	2.9719	0.256
Mature Eggplant/Ripe Tomato	2.31479	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07156
1-1-2/M82	1.07092	1
12-2/M82	N/A	N/A
12-4/M82	0.88262
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.69232
2-6/M82	0.99408	1
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	1.13783
5-3/M82	1.09676	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91048
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09408
IL2-6/WTpooled	1.27245	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.30283	0.362
IL12-4/WTpooled	0.88051	0.71
IL1-4/WTpooled	1.36403	1
WT/WTpooled	0.83377	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	0.91733	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86441	0.941
DC3000/delta hrp 6h	0.94244	0.95
DC3000/delta hrp 12h	1.03525	1
DC3000/delta hrp 24h	0.746	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11074	1
DC3000 delta B/DC3000 delta AB	1.25163	0.193

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77305	1
Exp 36h	0.89904	0.623
Exp 60h	0.78829	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97688
Var 0h	4.57549	0.782
Var 12h I row2-row1	1.09886	1
Var 12h NI row2-row1	1.37396	0.235
Var 36h I row2-row1	1.19686	0.601
Var 36h NI row2-row1	1.48946	1
Var 60h I row2-row1	1.27509
Var 60h NI row2-row1	0.98814	1
Time course 0hI-0hNI	0.84471	0.11
Time course 12hI-12hNI	1.0185	0.861
Time course 36hI-36hNI	1.28084	0.218
Time course 60hI-60hNI	1.00197	1

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)	1.06752	0.3
transgenic ySAMdc/azygous control (breaker)	1.42415	0.165
transgenic ySAMdc/azygous control (red)	1.04809	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00928	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38868	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.09362	0.083
Manapal/WT (break)	1.72007	0.183
Manapal/WT (red)	1.33953	0.15