Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.6.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87027	0.551
27DAP/17DAP	1.04264	1
39DAP/27DAP	0.89443	0.594
41DAP/39DAP	0.87784	0.555
42DAP/41DAP	1.07094	0.926
43DAP/42DAP	1.06049	1
47DAP/43DAP	1.02998	0.999
52DAP/47DAP	1.02403	0.88
57DAP/52DAP	1.24539	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85595	0.063
17DAP/reference	1.15828	0.066
27DAP/reference	1.0059	0.923
39DAP/reference	0.97458	0.638
41DAP/reference	1.09071	0.287
42DAP/reference	1.00019	0.628
43DAP/reference	1.0656	0.471
47DAP/reference	1.1653	0.037
52DAP/reference	1.04602	0.8
57DAP/reference	0.97826	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30258	0.431
27DAP/17DAP	0.93968	0.878
39DAP/27DAP	0.96298	0.804
41DAP/39DAP	0.92729	0.822
42DAP/41DAP	1.01495	0.787
43DAP/42DAP	1.30347	0.324
47DAP/43DAP	0.95641	0.805
52DAP/47DAP	0.97146	0.899
57DAP/52DAP	1.62638	0.148
57DAP/7DAP	1.30966	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26413	0.177
17DAP/reference	0.93924	0.167
27DAP/reference	1.10663	0.974
39DAP/reference	0.97811	0.474
41DAP/reference	1.17005	0.402
42DAP/reference	1.01405	0.791
43DAP/reference	1.24017	0.364
47DAP/reference	1.12389	0.195
52DAP/reference	0.9394	0.398
57DAP/reference	1.07245	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86788	0.164
17DAP/reference	0.87732	0.059
27DAP/reference	0.86959	0.021
39DAP/reference	0.93362	0.274
41DAP/reference	0.96589	0.256
42DAP/reference	1.22243	1
43DAP/reference	1.05145	1
47DAP/reference	0.97998	0.512
52DAP/reference	1.03703	0.882
57DAP/reference	1.01688	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28287	0.207
17DAP/reference	0.88232	0.255
27DAP/reference	3.13733	0.34
39DAP/reference	0.99068	0.693
41DAP/reference	1.1008	0.714
42DAP/reference	0.92748	0.22
43DAP/reference	0.85837	0.216
47DAP/reference	1.0476	0.585
52DAP/reference	1.24907	0.724
57DAP/reference	0.96208	0.553

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06727	1
26DAP/20DAP	1.50356	0.305
34DAP/26DAP	1.04612	1
51DAP/34DAP	0.96556	0.791
52DAP/51DAP	1.03738	0.848
53DAP/52DAP	1.10701	0.783
55DAP/53DAP	1.05565	0.964
57DAP/55DAP	0.96648	0.817
62DAP/57DAP	0.70228	0.088
68DAP/62DAP	0.92486	0.314
68DAP/14DAP	1.14378	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80619	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11607	0.417
Mature Green Tomato/Ripe Tomato	0.82816	0.411
Immature Eggplant/Mature Eggplant	5.52044	0.05
Ripe Pepper/Ripe Tomato	0.42357	0.293
Mature Eggplant/Ripe Tomato	0.35076

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.45575
12-2/M82	N/A	N/A
12-4/M82	0.88084	0.319
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	1.06158
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	0.91421	1
6-2/M82	0.78149
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.929
9-3-2/M82	0.79678

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.29355	0.277
IL2-6/WTpooled	0.8311	0.473
IL7-5/WTpooled	1.05308
IL7-3/WTpooled	1.17642	1
IL12-4/WTpooled	1.08541	0.839
IL1-4/WTpooled	1.12628	1
WT/WTpooled	0.94941	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	0.92571	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04776	0.921
DC3000/delta hrp 6h	0.96232	0.95
DC3000/delta hrp 12h	0.85699	1
DC3000/delta hrp 24h	1.10411	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85228	1
Exp 36h	1.69906	0.693
Exp 60h	1.25214	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99695	1
Var 0h	1.12509	0.782
Var 12h I row2-row1	0.86581	0.627
Var 12h NI row2-row1	0.92082	0.546
Var 36h I row2-row1	0.97058	1
Var 36h NI row2-row1	1.18331	0.229
Var 60h I row2-row1	0.89813	0.287
Var 60h NI row2-row1	1.19509	0.904
Time course 0hI-0hNI	0.93012	0.659
Time course 12hI-12hNI	0.98385	0.87
Time course 36hI-36hNI	0.94606	0.366
Time course 60hI-60hNI	0.5877	0.007

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)	0.9641	0.567
transgenic ySAMdc/azygous control (breaker)	0.92426	0.49
transgenic ySAMdc/azygous control (red)	0.91666	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21397	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1617	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05382	0.307
Manapal/WT (break)	1.02481	1
Manapal/WT (red)	1.10668	0.413