Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.19.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77877	0.206
27DAP/17DAP	0.93915	0.817
39DAP/27DAP	3.30691	0.025
41DAP/39DAP	2.12724	0.185
42DAP/41DAP	3.08321	0.029
43DAP/42DAP	1.08861	1
47DAP/43DAP	1.07495	1
52DAP/47DAP	0.53111	0.048
57DAP/52DAP	1.55263	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8777	0.317
17DAP/reference	0.97908	0.737
27DAP/reference	0.77966	0.194
39DAP/reference	0.97322	0.691
41DAP/reference	1.21555	0.48
42DAP/reference	4.00963	0.001
43DAP/reference	1.67618	0.015
47DAP/reference	2.38252	0.001
52DAP/reference	1.56497	0.031
57DAP/reference	1.79633	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92609	0.402
27DAP/17DAP	0.99009	0.943
39DAP/27DAP	1.4628	0.046
41DAP/39DAP	0.50887	0.018
42DAP/41DAP	1.5173	0.004
43DAP/42DAP	2.54286	0.013
47DAP/43DAP	0.85111	0.104
52DAP/47DAP	0.98392	0.919
57DAP/52DAP	1.03861	0.871
57DAP/7DAP	1.42874	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.23168	0.059
17DAP/reference	0.20719	0.011
27DAP/reference	0.2399	0.01
39DAP/reference	0.65851	0.034
41DAP/reference	0.39319	0.016
42DAP/reference	1.25155	1
43DAP/reference	1.67585	0.018
47DAP/reference	2.55329	0.014
52DAP/reference	0.60558	0.015
57DAP/reference	0.61272	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38765	0.238
17DAP/reference	0.60898	0.01
27DAP/reference	0.85216	0.229
39DAP/reference	0.85053	0.221
41DAP/reference	0.93689	0.307
42DAP/reference	0.84265	0.098
43DAP/reference	0.5017	0.016
47DAP/reference	0.96797	0.423
52DAP/reference	0.60399	0.004
57DAP/reference	0.7202	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.15738	0.019
17DAP/reference	0.78531	0.129
27DAP/reference	0.19611	0.02
39DAP/reference	0.38491	0.008
41DAP/reference	0.5286	0.019
42DAP/reference	4.45998	0.006
43DAP/reference	4.48998	0.006
47DAP/reference	3.82575	0.005
52DAP/reference	3.89078	0.027
57DAP/reference	1.43897	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02841	1
26DAP/20DAP	0.93463	0.512
34DAP/26DAP	1.05728	1
51DAP/34DAP	0.94152	0.667
52DAP/51DAP	1.02833	0.821
53DAP/52DAP	0.97188	0.807
55DAP/53DAP	1.06379	0.599
57DAP/55DAP	0.96217	0.823
62DAP/57DAP	1.11128	0.723
68DAP/62DAP	1.07457	0.897
68DAP/14DAP	1.17854

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	8.81913	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.52968
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.0918	0.224
Mature Eggplant/Ripe Tomato	0.05382	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95307	0.944
1-1-2/M82	0.98247	1
12-2/M82	0.95669	0.955
12-4/M82	1.0178	1
1-3/M82	1.00802	1
2-1-1/M82	0.87968	0.465
2-1/M82	0.93007	1
2-6/M82	0.93704	1
3-2/M82	1.07414	0.84
4-1-1/M82	1.01589	1
4-1/M82	1.74735	1
4-3-2/M82	0.96241	1
4-3/M82	0.91158	0.72
5-3/M82	0.97035	1
6-2/M82	0.92629	1
6-3/M82	0.9907	1
7-1/M82	1.01671	1
7-2/M82	0.85858	0.796
9-3-2/M82	0.73133	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94087	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.06469	0.362
IL12-4/WTpooled	1.02593	1
IL1-4/WTpooled	0.98883	1
WT/WTpooled	1.01688	0.789

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	0.88567	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01416	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.04602	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68242	0.024
DC3000 delta B/DC3000 delta AB	0.76616	0.027

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0151	1
Var 0h	1.0473	0.98
Var 12h I row2-row1	1.03345	1
Var 12h NI row2-row1	0.97081	0.82
Var 36h I row2-row1	1.00207	1
Var 36h NI row2-row1	1.08363	1
Var 60h I row2-row1	1.12004	0.523
Var 60h NI row2-row1	0.94408	0.977
Time course 0hI-0hNI	0.98838	0.991
Time course 12hI-12hNI	0.97515	0.745
Time course 36hI-36hNI	0.88476	0.096
Time course 60hI-60hNI	0.30761	0.006

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)	0.40537	0.246
transgenic ySAMdc/azygous control (breaker)	0.97118	1
transgenic ySAMdc/azygous control (red)	1.31151	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.26634	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69816	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.15347	1
Manapal/WT (red)	0.78742	0.36