Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.20.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98486	0.689
27DAP/17DAP	0.76382	0.251
39DAP/27DAP	1.17611	0.853
41DAP/39DAP	0.86667	0.49
42DAP/41DAP	1.27782	0.573
43DAP/42DAP	1.10136	1
47DAP/43DAP	1.05504	0.756
52DAP/47DAP	1.02725	0.98
57DAP/52DAP	0.95345	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9594	0.211
17DAP/reference	0.98008	0.664
27DAP/reference	0.95016	0.484
39DAP/reference	0.99356	0.901
41DAP/reference	1.04341	0.808
42DAP/reference	0.97558	0.305
43DAP/reference	1.06512	0.445
47DAP/reference	1.15438	0.003
52DAP/reference	1.0465	0.84
57DAP/reference	1.10839	0.195

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19618	0.365
27DAP/17DAP	1.0901	0.771
39DAP/27DAP	0.95563	0.732
41DAP/39DAP	1.10613	0.735
42DAP/41DAP	0.8588	0.206
43DAP/42DAP	0.56644	0.023
47DAP/43DAP	0.94436	0.75
52DAP/47DAP	1.22371	0.366
57DAP/52DAP	1.07781	0.618
57DAP/7DAP	0.836	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14387	0.332
17DAP/reference	1.21336	0.693
27DAP/reference	1.17929	0.088
39DAP/reference	1.50377	0.01
41DAP/reference	1.37035	0.037
42DAP/reference	1.47736	0.013
43DAP/reference	1.58503	0.007
47DAP/reference	1.23579	0.2
52DAP/reference	1.3788	0.008
57DAP/reference	1.23627	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92948	0.268
17DAP/reference	0.88085	0.046
27DAP/reference	0.93367	0.317
39DAP/reference	0.83797	0.108
41DAP/reference	0.93153	0.364
42DAP/reference	1.00341	1
43DAP/reference	0.99632	0.721
47DAP/reference	1.20846	0.043
52DAP/reference	0.94674	0.28
57DAP/reference	1.1893	0.094

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10129	0.273
17DAP/reference	1.06395	0.824
27DAP/reference	1.30704	0.02
39DAP/reference	1.32181	0.026
41DAP/reference	1.37444	0.029
42DAP/reference	1.18342	0.091
43DAP/reference	1.1603	0.336
47DAP/reference	1.21627	0.05
52DAP/reference	1.39393	0.083
57DAP/reference	1.15767	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19349	0.945
26DAP/20DAP	1.23135	0.259
34DAP/26DAP	0.93178	0.811
51DAP/34DAP	1.32129	0.261
52DAP/51DAP	1.24205	0.708
53DAP/52DAP	0.91428	0.807
55DAP/53DAP	0.98118	0.876
57DAP/55DAP	1.01692	0.935
62DAP/57DAP	1.0985	1
68DAP/62DAP	0.80174	0.227
68DAP/14DAP	0.89774	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95974	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.18369	0.055
Mature Green Tomato/Ripe Tomato	0.71383	0.096
Immature Eggplant/Mature Eggplant	2.67174	0.056
Ripe Pepper/Ripe Tomato	4.58698	1
Mature Eggplant/Ripe Tomato	0.48728

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82502	0.958
12-2/M82	1.40784
12-4/M82	0.85645	0.619
1-3/M82	0.99152
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.09493	0.695
3-2/M82	0.96971	1
4-1-1/M82	N/A	N/A
4-1/M82	1.26511	0.444
4-3-2/M82	0.84685
4-3/M82	1.83239	0.268
5-3/M82	0.8414	0.642
6-2/M82	N/A	N/A
6-3/M82	0.9205
7-1/M82	0.79677	0.803
7-2/M82	0.63538
9-3-2/M82	1.03841

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.07802
WT/WTpooled	N/A	N/A

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	1.02088	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11154	0.914
DC3000/delta hrp 6h	1.15588	0.857
DC3000/delta hrp 12h	0.96887	1
DC3000/delta hrp 24h	1.01861	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.69963	0.023
DC3000 delta B/DC3000 delta AB	0.64596	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07365	1
Exp 36h	1.03106	1
Exp 60h	0.98841	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.88719	0.713
Var 36h I row2-row1	0.87173
Var 36h NI row2-row1	1.07203	1
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.12579	0.904
Time course 0hI-0hNI	1.02701	1
Time course 12hI-12hNI	0.94374	0.374
Time course 36hI-36hNI	0.69426	0.023
Time course 60hI-60hNI	0.19164	0.005

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)	0.82489	0.239
transgenic ySAMdc/azygous control (breaker)	0.84524	0.15
transgenic ySAMdc/azygous control (red)	1.10113	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01428	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.35493	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.0823	0.09
Manapal/WT (break)	2.22269	0.14
Manapal/WT (red)	1.37705	0.134