Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.6.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82777	0.166
27DAP/17DAP	1.17253	0.885
39DAP/27DAP	0.82703	0.549
41DAP/39DAP	0.86598	0.475
42DAP/41DAP	1.17728	0.841
43DAP/42DAP	1.03895	1
47DAP/43DAP	0.88335	0.603
52DAP/47DAP	0.98823	0.92
57DAP/52DAP	1.10448	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99254	0.693
17DAP/reference	0.95629	0.321
27DAP/reference	0.96309	0.304
39DAP/reference	0.96911	0.455
41DAP/reference	0.98172	0.667
42DAP/reference	1.04224	0.398
43DAP/reference	1.0825	0.064
47DAP/reference	0.90558	0.015
52DAP/reference	0.90484	0.177
57DAP/reference	0.77495	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90931	0.277
27DAP/17DAP	1.10015	0.598
39DAP/27DAP	0.92251	0.394
41DAP/39DAP	0.9755	0.968
42DAP/41DAP	1.01165	0.991
43DAP/42DAP	1.07504	0.122
47DAP/43DAP	1.01386	0.956
52DAP/47DAP	0.99033	0.93
57DAP/52DAP	0.95093	0.476
57DAP/7DAP	1.053	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96075	0.168
17DAP/reference	0.91842	0.044
27DAP/reference	0.96069	0.146
39DAP/reference	0.86738	0.018
41DAP/reference	0.87649	0.012
42DAP/reference	0.90562	0.046
43DAP/reference	0.8443	0.015
47DAP/reference	0.88144	0.035
52DAP/reference	0.88129	0.033
57DAP/reference	0.84878	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09698	0.36
17DAP/reference	1.14245	0.07
27DAP/reference	0.96123	0.452
39DAP/reference	0.91481	0.144
41DAP/reference	0.87194	0.03
42DAP/reference	0.86274	0.032
43DAP/reference	1.21248	0.023
47DAP/reference	0.95595	0.232
52DAP/reference	1.0199	1
57DAP/reference	1.23299	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00365	1
17DAP/reference	1.00415	0.934
27DAP/reference	0.89032	0.03
39DAP/reference	0.85592	0.035
41DAP/reference	0.87071	0.033
42DAP/reference	0.77568	0.071
43DAP/reference	0.79843	0.131
47DAP/reference	1.05919	1
52DAP/reference	0.83348	0.186
57DAP/reference	0.55223	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07494	0.945
26DAP/20DAP	1.05054	0.839
34DAP/26DAP	0.93371	0.712
51DAP/34DAP	1.03773	0.869
52DAP/51DAP	0.96184	1
53DAP/52DAP	1.03924	0.921
55DAP/53DAP	0.99969	0.951
57DAP/55DAP	1.0377	0.927
62DAP/57DAP	1.18564	0.133
68DAP/62DAP	0.78247	0.245
68DAP/14DAP	0.78201	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70458	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72418	0.215
Mature Green Tomato/Ripe Tomato	1.29635	0.523
Immature Eggplant/Mature Eggplant	0.68243	0.077
Ripe Pepper/Ripe Tomato	3.56839	1
Mature Eggplant/Ripe Tomato	2.77549	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04564	1
1-1-2/M82	1.03977	1
12-2/M82	1.06594
12-4/M82	0.93482	0.319
1-3/M82	0.8118
2-1-1/M82	0.92991
2-1/M82	0.94344
2-6/M82	1.07164	1
3-2/M82	1.18115
4-1-1/M82	N/A	N/A
4-1/M82	1.13822
4-3-2/M82	0.91838	0.487
4-3/M82	0.70933	0.72
5-3/M82	0.97814	1
6-2/M82	N/A	N/A
6-3/M82	1.17596
7-1/M82	0.9999	1
7-2/M82	1.19521	1
9-3-2/M82	1.06888

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.12141	1
IL7-5/WTpooled	1.32528
IL7-3/WTpooled	1.0535	1
IL12-4/WTpooled	1.04969	0.891
IL1-4/WTpooled	1.00392	1
WT/WTpooled	1.03869	0.874

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	1.06207	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09719	0.75
DC3000/delta hrp 6h	0.73635	0.914
DC3000/delta hrp 12h	1.10835	1
DC3000/delta hrp 24h	1.0354	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01968	0.229
DC3000 delta B/DC3000 delta AB	0.92134	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.10605	1
Exp 60h	0.98207	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02111	1
Var 0h	0.36746	1
Var 12h I row2-row1	1.084	0.654
Var 12h NI row2-row1	1.09913	1
Var 36h I row2-row1	0.94698	1
Var 36h NI row2-row1	1.08981	1
Var 60h I row2-row1	0.83456	0.292
Var 60h NI row2-row1	1.16647	0.691
Time course 0hI-0hNI	0.99969	1
Time course 12hI-12hNI	0.9653	0.746
Time course 36hI-36hNI	0.9357	0.246
Time course 60hI-60hNI	1.09533	0.495

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)	0.95863	0.315
transgenic ySAMdc/azygous control (breaker)	0.95284	1
transgenic ySAMdc/azygous control (red)	1.01386	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02482	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02367	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73887	0.172
Manapal/WT (break)	1.23713	0.381
Manapal/WT (red)	1.18948	0.413