Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15069	0.697
27DAP/17DAP	0.50988	0.038
39DAP/27DAP	0.71155	0.414
41DAP/39DAP	0.60246	0.045
42DAP/41DAP	0.67281	0.774
43DAP/42DAP	1.19896	0.867
47DAP/43DAP	0.34641	0.049
52DAP/47DAP	0.66347	0.239
57DAP/52DAP	1.05808	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58128	0.035
17DAP/reference	0.45748	0.016
27DAP/reference	0.41731	0.013
39DAP/reference	0.23009	0.009
41DAP/reference	0.21038	0.008
42DAP/reference	0.28216	0.001
43DAP/reference	0.11945	0.012
47DAP/reference	0.136	0.001
52DAP/reference	0.14196	0.012
57DAP/reference	0.1813	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.0961	0.036
27DAP/17DAP	0.72247	0.295
39DAP/27DAP	0.2352	0.028
41DAP/39DAP	1.4628	0.044
42DAP/41DAP	0.75521	0.026
43DAP/42DAP	0.37378	0.022
47DAP/43DAP	0.65844	0.03
52DAP/47DAP	0.7184	0.29
57DAP/52DAP	0.90328	0.546
57DAP/7DAP	0.75779	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96325	0.495
17DAP/reference	0.69747	0.011
27DAP/reference	0.46849	0.01
39DAP/reference	0.34937	0.011
41DAP/reference	0.27303	0.009
42DAP/reference	0.34194	0.01
43DAP/reference	0.1895	0.009
47DAP/reference	0.17848	0.026
52DAP/reference	0.25116	0.01
57DAP/reference	0.26957	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.3594	0.007
17DAP/reference	0.34347	0.011
27DAP/reference	0.47191	0.018
39DAP/reference	0.24336	0.008
41DAP/reference	0.32521	0.005
42DAP/reference	0.42322	0.016
43DAP/reference	0.14077	0.001
47DAP/reference	0.23836	0.01
52DAP/reference	0.08654	0.003
57DAP/reference	0.13514	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.08927	0.018
17DAP/reference	1.89897	0.14
27DAP/reference	1.42315	0.059
39DAP/reference	1.07004	0.987
41DAP/reference	0.71062	0.031
42DAP/reference	0.40422	0.015
43DAP/reference	0.44415	0.016
47DAP/reference	0.25885	0.004
52DAP/reference	0.24179	0.05
57DAP/reference	1.10721	0.933

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.79584	0.966
26DAP/20DAP	1.09684	0.839
34DAP/26DAP	0.78404	0.092
51DAP/34DAP	0.4247	0.049
52DAP/51DAP	1.03063	0.873
53DAP/52DAP	0.56464	0.049
55DAP/53DAP	0.71891	0.016
57DAP/55DAP	0.78681	0.3
62DAP/57DAP	1.82747	0.005
68DAP/62DAP	0.88091	0.7
68DAP/14DAP	0.37698	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.32646	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.09879	0.058
Mature Green Tomato/Ripe Tomato	36.3182	0.015
Immature Eggplant/Mature Eggplant	0.43981	0.057
Ripe Pepper/Ripe Tomato	21.1441	0.233
Mature Eggplant/Ripe Tomato	56.2978	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30952
1-1-2/M82	0.7024
12-2/M82	0.36832
12-4/M82	0.65149
1-3/M82	N/A	N/A
2-1-1/M82	1.22684
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.63405
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	1.99907	1
6-2/M82	1.19636
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74062	0.243
IL2-6/WTpooled	0.78929	0.473
IL7-5/WTpooled	1.00968	1
IL7-3/WTpooled	0.99485	1
IL12-4/WTpooled	0.9406	0.71
IL1-4/WTpooled	0.88768	0.444
WT/WTpooled	0.9811	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	1.14542	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96148	1
DC3000/delta hrp 6h	0.89638	0.95
DC3000/delta hrp 12h	1.00079	1
DC3000/delta hrp 24h	0.97466	0.924

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03117
DC3000 delta B/DC3000 delta AB	0.69914	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01432	1
Exp 36h	1.00642	1
Exp 60h	0.97033	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9936	1
Var 0h	1.09689	0.782
Var 12h I row2-row1	0.96695	0.856
Var 12h NI row2-row1	1.03902	1
Var 36h I row2-row1	0.98439	1
Var 36h NI row2-row1	0.91244	0.478
Var 60h I row2-row1	1.33744	0.543
Var 60h NI row2-row1	0.92948	0.977
Time course 0hI-0hNI	1.06478	0.833
Time course 12hI-12hNI	1.10365	0.392
Time course 36hI-36hNI	1.04647	0.881
Time course 60hI-60hNI	0.75516	0.081

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)	1.16074	0.699
transgenic ySAMdc/azygous control (breaker)	4.56749	0.162
transgenic ySAMdc/azygous control (red)	1.49611	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.48648	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08561	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	19.2499	0.087
Manapal/WT (break)	16.7603	0.126
Manapal/WT (red)	2.60774	1