Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.1.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99862	0.823
27DAP/17DAP	1.17359	0.847
39DAP/27DAP	1.02257	0.857
41DAP/39DAP	1.61879	0.451
42DAP/41DAP	0.83764	1
43DAP/42DAP	0.92686	0.829
47DAP/43DAP	0.922	0.595
52DAP/47DAP	1.5126	0.516
57DAP/52DAP	0.87629	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89153	0.326
17DAP/reference	0.97649	0.393
27DAP/reference	0.92212	0.075
39DAP/reference	0.9954	0.921
41DAP/reference	0.92855	0.434
42DAP/reference	0.93789	0.099
43DAP/reference	1.01289	0.957
47DAP/reference	0.93268	0.018
52DAP/reference	0.90894	0.093
57DAP/reference	0.86651	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84249	0.27
27DAP/17DAP	1.04672	0.976
39DAP/27DAP	1.06697	0.643
41DAP/39DAP	1.17183	0.837
42DAP/41DAP	0.75635	0.092
43DAP/42DAP	1.01503	1
47DAP/43DAP	0.83481	0.382
52DAP/47DAP	1.05154	1
57DAP/52DAP	0.8369	0.346
57DAP/7DAP	1.38255	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00627	1
17DAP/reference	1.25492	0.022
27DAP/reference	1.22736	0.011
39DAP/reference	1.35824	0.007
41DAP/reference	1.39851	0.019
42DAP/reference	1.3471	0.011
43DAP/reference	1.27148	0.008
47DAP/reference	1.52155	0.421
52DAP/reference	1.10324	0.352
57DAP/reference	1.13549	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16021	0.053
17DAP/reference	1.13956	0.043
27DAP/reference	0.97509	0.537
39DAP/reference	1.27184	0.783
41DAP/reference	1.0292	1
42DAP/reference	0.80886	0.02
43DAP/reference	1.10393	0.247
47DAP/reference	0.86848	0.023
52DAP/reference	0.90755	0.407
57DAP/reference	1.32462	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99717	0.75
17DAP/reference	1.0511	0.45
27DAP/reference	1.10068	0.271
39DAP/reference	1.09011	0.218
41DAP/reference	1.2688	0.017
42DAP/reference	1.08901	0.356
43DAP/reference	1.19654	0.154
47DAP/reference	0.98096	0.478
52DAP/reference	1.02182	0.876
57DAP/reference	0.92188	0.238

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91247	1
26DAP/20DAP	0.87223	1
34DAP/26DAP	0.69357	0.256
51DAP/34DAP	0.9452	0.688
52DAP/51DAP	1.37585	0.087
53DAP/52DAP	0.94362	0.817
55DAP/53DAP	1.22109	0.671
57DAP/55DAP	0.75422	0.197
62DAP/57DAP	1.16001	0.057
68DAP/62DAP	0.96195	0.769
68DAP/14DAP	1.16063	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01439	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.93074	0.446
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.11168
Mature Eggplant/Ripe Tomato	0.36222	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12489	0.877
1-1-2/M82	0.80476
12-2/M82	1.30256
12-4/M82	1.5654
1-3/M82	0.94729	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.84673	0.501
3-2/M82	0.76229
4-1-1/M82	1.09707
4-1/M82	1.49883
4-3-2/M82	0.83826
4-3/M82	0.84205	0.72
5-3/M82	0.99144	1
6-2/M82	N/A	N/A
6-3/M82	1.04063
7-1/M82	N/A	N/A
7-2/M82	0.81259	0.57
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21628	1
IL2-6/WTpooled	0.60694
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87827	0.31
IL12-4/WTpooled	0.89343	1
IL1-4/WTpooled	1.07499	1
WT/WTpooled	1.03506	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	0.98438	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06897	0.692
DC3000/delta hrp 6h	1.09297	1
DC3000/delta hrp 12h	0.97225	1
DC3000/delta hrp 24h	1.01228	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90965
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02949	1
Exp 36h	0.97859	1
Exp 60h	1.01532	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9747	1
Var 0h	1.1528	0.325
Var 12h I row2-row1	0.9949	1
Var 12h NI row2-row1	0.8996	0.33
Var 36h I row2-row1	0.91695	0.805
Var 36h NI row2-row1	1.01645	1
Var 60h I row2-row1	1.03106	1
Var 60h NI row2-row1	1.04957	1
Time course 0hI-0hNI	0.98672	0.981
Time course 12hI-12hNI	1.28172	0.025
Time course 36hI-36hNI	1.56168	0.005
Time course 60hI-60hNI	2.22499	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)	1.13829	0.347
transgenic ySAMdc/azygous control (breaker)	1.07007	0.248
transgenic ySAMdc/azygous control (red)	1.03448	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99701	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85517	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13122	0.307
Manapal/WT (break)	0.83155	0.381
Manapal/WT (red)	1.24076	0.413