Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.13.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74108	0.19
27DAP/17DAP	1.05935	1
39DAP/27DAP	1.79736	0.56
41DAP/39DAP	0.91943	0.685
42DAP/41DAP	1.13193	0.962
43DAP/42DAP	1.1882	1
47DAP/43DAP	1.18823	0.633
52DAP/47DAP	1.09975	0.948
57DAP/52DAP	1.32039	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97044	0.489
17DAP/reference	0.97543	0.567
27DAP/reference	0.99942	0.904
39DAP/reference	1.09173	0.045
41DAP/reference	1.13122	0.025
42DAP/reference	0.94671	0.151
43DAP/reference	1.02521	0.518
47DAP/reference	0.95866	0.279
52DAP/reference	0.90906	0.215
57DAP/reference	0.94789	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00608	1
27DAP/17DAP	0.90322	0.446
39DAP/27DAP	1.10594	0.441
41DAP/39DAP	0.95521	0.893
42DAP/41DAP	1.03699	1
43DAP/42DAP	1.04421	0.554
47DAP/43DAP	1.00092	0.99
52DAP/47DAP	1.01331	0.979
57DAP/52DAP	0.90951	0.299
57DAP/7DAP	1.19814	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21025	0.115
17DAP/reference	1.84222	0.007
27DAP/reference	1.62461	0.01
39DAP/reference	1.72196	0.007
41DAP/reference	1.83688	0.01
42DAP/reference	1.75032	0.009
43DAP/reference	1.88685	0.009
47DAP/reference	1.34745	0.279
52DAP/reference	1.45587	0.008
57DAP/reference	1.7808	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10149	0.449
17DAP/reference	1.2776	0.045
27DAP/reference	1.18886	0.089
39DAP/reference	1.1049	0.316
41DAP/reference	1.08998	0.153
42DAP/reference	1.17868	0.029
43DAP/reference	1.42815	0.407
47DAP/reference	1.23248	0.034
52DAP/reference	1.34157	0.032
57DAP/reference	1.31782	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42937	0.047
17DAP/reference	1.29797	0.264
27DAP/reference	1.92316	0.018
39DAP/reference	1.76197	0.005
41DAP/reference	1.66736	0.007
42DAP/reference	1.57083	0.011
43DAP/reference	1.44643	0.085
47DAP/reference	1.17062	0.006
52DAP/reference	1.6828	0.153
57DAP/reference	1.07396	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07742	0.966
26DAP/20DAP	0.75555	0.512
34DAP/26DAP	0.89128	0.753
51DAP/34DAP	0.96545	0.844
52DAP/51DAP	0.96409	1
53DAP/52DAP	0.95394	0.783
55DAP/53DAP	0.96529	0.761
57DAP/55DAP	1.07698	0.997
62DAP/57DAP	1.13266	0.723
68DAP/62DAP	0.77877	0.406
68DAP/14DAP	1.2602	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98777	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.79369	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.68604	0.224
Mature Eggplant/Ripe Tomato	1.03012	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03198	0.877
1-1-2/M82	1.00345	1
12-2/M82	1.13288
12-4/M82	1.78448
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	0.96769	1
3-2/M82	N/A	N/A
4-1-1/M82	0.99588	1
4-1/M82	1.02628	0.853
4-3-2/M82	N/A	N/A
4-3/M82	0.94258	1
5-3/M82	1.14352	1
6-2/M82	0.90907
6-3/M82	1.1858	1
7-1/M82	N/A	N/A
7-2/M82	1.01389	1
9-3-2/M82	0.72595

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97756
IL2-6/WTpooled	1.16045	0.659
IL7-5/WTpooled	1.74531	0.75
IL7-3/WTpooled	1.01898	1
IL12-4/WTpooled	1.00385	1
IL1-4/WTpooled	1.0532
WT/WTpooled	0.97931	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	1.12689	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11118	0.921
DC3000/delta hrp 6h	1.01315	0.95
DC3000/delta hrp 12h	1.13316	1
DC3000/delta hrp 24h	1.27297	0.411

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	1.287	0.406

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	1.20312	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94241	1
Var 0h	0.9286	1
Var 12h I row2-row1	1.11045	0.204
Var 12h NI row2-row1	0.67336	0.713
Var 36h I row2-row1	0.84904	0.805
Var 36h NI row2-row1	1.01782
Var 60h I row2-row1	1.78872	0.562
Var 60h NI row2-row1	1.39509	0.904
Time course 0hI-0hNI	1.07289	0.833
Time course 12hI-12hNI	1.01034	0.885
Time course 36hI-36hNI	0.99782	0.742
Time course 60hI-60hNI	1.04304	0.575

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)	0.99363	0.862
transgenic ySAMdc/azygous control (breaker)	0.94081	0.251
transgenic ySAMdc/azygous control (red)	0.98356	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98845	0.552

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04235	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01434	1
Manapal/WT (break)	0.92262	1
Manapal/WT (red)	1.18299	0.413