Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9047	0.543
27DAP/17DAP	1.63139	0.413
39DAP/27DAP	1.075	0.99
41DAP/39DAP	1.47858	0.398
42DAP/41DAP	1.47992	0.672
43DAP/42DAP	0.70414	0.409
47DAP/43DAP	1.04912	0.999
52DAP/47DAP	1.21671	0.915
57DAP/52DAP	0.84148	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05249	0.544
17DAP/reference	1.05009	0.239
27DAP/reference	1.00842	0.904
39DAP/reference	1.02767	0.691
41DAP/reference	1.16575	0.158
42DAP/reference	0.89367	0.018
43DAP/reference	1.05209	0.569
47DAP/reference	0.8838	0.018
52DAP/reference	0.85541	0.162
57DAP/reference	0.79644	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84141	0.27
27DAP/17DAP	0.91034	0.648
39DAP/27DAP	1.15516	0.353
41DAP/39DAP	1.5117	0.266
42DAP/41DAP	0.85457	0.143
43DAP/42DAP	1.105	0.513
47DAP/43DAP	1.12225	0.678
52DAP/47DAP	0.87252	0.321
57DAP/52DAP	1.03435	0.891
57DAP/7DAP	1.22143	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85512	0.129
17DAP/reference	0.83419	0.013
27DAP/reference	0.82116	0.01
39DAP/reference	0.80082	0.011
41DAP/reference	0.7613	0.02
42DAP/reference	0.7435	0.011
43DAP/reference	0.69283	0.018
47DAP/reference	0.88143	0.383
52DAP/reference	0.64599	0.03
57DAP/reference	0.72225	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09018	0.443
17DAP/reference	1.04739	0.584
27DAP/reference	0.91212	0.282
39DAP/reference	0.81955	0.113
41DAP/reference	0.87491	0.121
42DAP/reference	0.80189	0.035
43DAP/reference	1.19561	0.255
47DAP/reference	0.97081	0.446
52DAP/reference	0.956	0.187
57DAP/reference	1.36384	0.14

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97472	0.489
17DAP/reference	1.05592	0.685
27DAP/reference	0.80242	0.026
39DAP/reference	0.82972	0.022
41DAP/reference	0.82801	0.033
42DAP/reference	0.7632	0.016
43DAP/reference	0.72738	0.048
47DAP/reference	0.97501	0.525
52DAP/reference	0.86784	0.319
57DAP/reference	0.58579	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07876	0.966
26DAP/20DAP	0.86611	0.317
34DAP/26DAP	1.04929	1
51DAP/34DAP	0.90652	0.41
52DAP/51DAP	0.99497	1
53DAP/52DAP	1.00239	1
55DAP/53DAP	0.9853	0.852
57DAP/55DAP	1.03755	0.969
62DAP/57DAP	1.31252	0.303
68DAP/62DAP	0.84768	0.429
68DAP/14DAP	0.78178	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03246	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81431
Mature Green Tomato/Ripe Tomato	0.95806	0.611
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.74845

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93729	0.944
1-1-2/M82	0.85118	1
12-2/M82	1.16233	1
12-4/M82	1.05313
1-3/M82	0.81267	0.441
2-1-1/M82	1.31413
2-1/M82	N/A	N/A
2-6/M82	1.26226	0.594
3-2/M82	0.77236
4-1-1/M82	0.99633	1
4-1/M82	1.30914
4-3-2/M82	0.99422
4-3/M82	0.63169
5-3/M82	1.03709	1
6-2/M82	0.9333	1
6-3/M82	1.13486	1
7-1/M82	1.07898
7-2/M82	0.95263	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96245	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.21115	1
IL12-4/WTpooled	0.94815	0.71
IL1-4/WTpooled	1.01995
WT/WTpooled	0.99891	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	3.557	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98409	1
DC3000/delta hrp 6h	3.58338
DC3000/delta hrp 12h	1.19873	1
DC3000/delta hrp 24h	1.31681	0.06

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.73703	0.042
DC3000 delta B/DC3000 delta AB	1.69287	0.123

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	3.9269	0.349
Exp 60h	6.45801	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02119	1
Var 0h	0.91925	1
Var 12h I row2-row1	1.1666	0.272
Var 12h NI row2-row1	0.91231	0.546
Var 36h I row2-row1	1.03133	1
Var 36h NI row2-row1	0.85366	0.549
Var 60h I row2-row1	0.9729	0.952
Var 60h NI row2-row1	1.18156	0.904
Time course 0hI-0hNI	1.17287	0.63
Time course 12hI-12hNI	1.17598	0.237
Time course 36hI-36hNI	3.79167	0.005
Time course 60hI-60hNI	5.77752	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)	4.03331	0.261
transgenic ySAMdc/azygous control (breaker)	2.21836	1
transgenic ySAMdc/azygous control (red)	1.38722	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01045	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.15565	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.03122	1
Manapal/WT (red)	0.50489	0.181