Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.18.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03635	0.779
27DAP/17DAP	3.67816	0.047
39DAP/27DAP	1.09218	1
41DAP/39DAP	0.86141	0.473
42DAP/41DAP	1.35763	0.471
43DAP/42DAP	0.90266	0.721
47DAP/43DAP	1.21845	0.647
52DAP/47DAP	0.85516	0.612
57DAP/52DAP	1.13604	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90248	0.277
17DAP/reference	1.03587	0.492
27DAP/reference	1.01666	0.847
39DAP/reference	0.97754	0.68
41DAP/reference	1.08814	0.265
42DAP/reference	0.85856	0.012
43DAP/reference	1.06214	0.617
47DAP/reference	0.88546	0.021
52DAP/reference	0.69454	0.025
57DAP/reference	0.75688	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09474	0.508
27DAP/17DAP	1.02899	0.915
39DAP/27DAP	1.09515	0.483
41DAP/39DAP	0.99026	0.997
42DAP/41DAP	0.96119	0.715
43DAP/42DAP	1.02276	0.664
47DAP/43DAP	1.10326	0.135
52DAP/47DAP	1.04992	0.816
57DAP/52DAP	1.02169	0.895
57DAP/7DAP	1.23911	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90729	0.115
17DAP/reference	0.89536	0.144
27DAP/reference	0.83567	0.037
39DAP/reference	0.81567	0.015
41DAP/reference	0.96569	0.449
42DAP/reference	0.92959	0.262
43DAP/reference	0.85975	0.121
47DAP/reference	0.88954	0.222
52DAP/reference	0.93713	0.278
57DAP/reference	1.00423	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01393	1
17DAP/reference	0.90867	0.124
27DAP/reference	0.74109	0.031
39DAP/reference	0.75161	0.031
41DAP/reference	0.75722	0.042
42DAP/reference	0.77661	0.018
43DAP/reference	0.85518	0.121
47DAP/reference	0.8059	0.014
52DAP/reference	0.8495	0.009
57DAP/reference	0.96405	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89163	0.135
17DAP/reference	0.97285	0.658
27DAP/reference	0.97011	0.539
39DAP/reference	0.94807	0.328
41DAP/reference	0.88025	0.148
42DAP/reference	0.9366	0.552
43DAP/reference	0.81318	0.12
47DAP/reference	0.92513	0.306
52DAP/reference	0.90828	0.424
57DAP/reference	0.48488	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.06858	0.966
26DAP/20DAP	1.25464	0.518
34DAP/26DAP	0.91186	0.399
51DAP/34DAP	1.26641	0.089
52DAP/51DAP	1.08012	0.467
53DAP/52DAP	1.01766	0.944
55DAP/53DAP	1.04048	0.911
57DAP/55DAP	0.88613	0.433
62DAP/57DAP	1.00386	1
68DAP/62DAP	0.98163	0.863
68DAP/14DAP	1.03446	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81006	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.30099	0.058
Mature Green Tomato/Ripe Tomato	0.95206	0.446
Immature Eggplant/Mature Eggplant	1.5799	0.053
Ripe Pepper/Ripe Tomato	1.51976	0.258
Mature Eggplant/Ripe Tomato	1.88245	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94726	0.944
1-1-2/M82	0.98927	1
12-2/M82	1.10187	1
12-4/M82	0.88617
1-3/M82	0.94946	1
2-1-1/M82	1.1067	0.295
2-1/M82	0.9269	0.74
2-6/M82	1.0968	0.695
3-2/M82	0.53114	0.752
4-1-1/M82	1.01649	1
4-1/M82	1.56831	1
4-3-2/M82	0.93511	1
4-3/M82	1.19659	1
5-3/M82	1.08255	1
6-2/M82	1.14962	1
6-3/M82	0.90854	1
7-1/M82	1.38461
7-2/M82	1.12127	1
9-3-2/M82	1.1905	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69138	0.247
IL2-6/WTpooled	0.92159	0.473
IL7-5/WTpooled	0.77742	1
IL7-3/WTpooled	1.33224	1
IL12-4/WTpooled	0.79167	0.71
IL1-4/WTpooled	0.87775	0.834
WT/WTpooled	0.96002	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	1.04523	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12048	0.774
DC3000/delta hrp 6h	1.31002	1
DC3000/delta hrp 12h	1.00181	1
DC3000/delta hrp 24h	1.02687	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20549	0.29
DC3000 delta B/DC3000 delta AB	1.12212	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97049	1
Exp 36h	1.21584	1
Exp 60h	1.23721	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03756	1
Var 0h	0.90979	1
Var 12h I row2-row1	1.01372	0.795
Var 12h NI row2-row1	1.09771	1
Var 36h I row2-row1	1.0612	1
Var 36h NI row2-row1	1.53019	1
Var 60h I row2-row1	0.92078	0.439
Var 60h NI row2-row1	0.99416	1
Time course 0hI-0hNI	1.05294	0.799
Time course 12hI-12hNI	1.03106	0.803
Time course 36hI-36hNI	0.93216	0.317
Time course 60hI-60hNI	1.5495	0.008

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)	0.96563	0.314
transgenic ySAMdc/azygous control (breaker)	0.75345	0.15
transgenic ySAMdc/azygous control (red)	1.05179	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05007	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66938	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91559	1
Manapal/WT (break)	0.76743	0.299
Manapal/WT (red)	0.9086	0.503