Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.10.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32831	0.414
27DAP/17DAP	0.86558	0.661
39DAP/27DAP	0.77893	0.462
41DAP/39DAP	0.84136	0.394
42DAP/41DAP	1.12091	0.737
43DAP/42DAP	1.30514	0.284
47DAP/43DAP	1.2666	0.442
52DAP/47DAP	0.70845	0.299
57DAP/52DAP	1.09161	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69991	0.032
17DAP/reference	0.63065	0.012
27DAP/reference	0.61681	0.016
39DAP/reference	0.62278	0.027
41DAP/reference	0.46666	0.01
42DAP/reference	0.49656	0.001
43DAP/reference	0.38127	0.012
47DAP/reference	0.47351	0.001
52DAP/reference	0.45929	0.015
57DAP/reference	0.46356	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37481	0.154
27DAP/17DAP	0.86585	0.58
39DAP/27DAP	0.73256	0.042
41DAP/39DAP	0.91483	0.781
42DAP/41DAP	1.10967	0.916
43DAP/42DAP	0.76238	0.07
47DAP/43DAP	1.0262	0.973
52DAP/47DAP	1.24248	0.474
57DAP/52DAP	1.54454	0.083
57DAP/7DAP	1.69573	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97798	0.55
17DAP/reference	0.69932	0.012
27DAP/reference	0.50459	0.01
39DAP/reference	0.42411	0.011
41DAP/reference	0.33038	0.009
42DAP/reference	0.29985	0.01
43DAP/reference	0.23878	0.009
47DAP/reference	0.29522	0.026
52DAP/reference	0.28027	0.009
57DAP/reference	0.32431	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.57289	0.007
17DAP/reference	0.57724	0.007
27DAP/reference	0.64833	0.024
39DAP/reference	0.39322	0.008
41DAP/reference	0.41982	0.005
42DAP/reference	0.47227	0.011
43DAP/reference	0.26212	0.002
47DAP/reference	0.3728	0.008
52DAP/reference	0.29409	0.003
57DAP/reference	0.26089	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68191	0.018
17DAP/reference	1.68791	0.137
27DAP/reference	1.06972	0.721
39DAP/reference	0.93733	0.299
41DAP/reference	0.61857	0.02
42DAP/reference	0.53169	0.014
43DAP/reference	0.44599	0.016
47DAP/reference	0.33009	0.004
52DAP/reference	0.35717	0.05
57DAP/reference	0.69712	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09565	0.966
26DAP/20DAP	1.34565	0.253
34DAP/26DAP	0.9974	1
51DAP/34DAP	1.02697	0.898
52DAP/51DAP	0.80597	1
53DAP/52DAP	0.86125	0.301
55DAP/53DAP	1.021	0.989
57DAP/55DAP	1.25474	0.87
62DAP/57DAP	1.23559	0.767
68DAP/62DAP	1.1431	0.85
68DAP/14DAP	0.70413	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74464	0.062

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.70887	0.058
Mature Green Tomato/Ripe Tomato	2.48254	0.015
Immature Eggplant/Mature Eggplant	0.34586	0.062
Ripe Pepper/Ripe Tomato	52.1932	1
Mature Eggplant/Ripe Tomato	1.15587	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.9424
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.37161
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
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	1.16935	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03145	1
IL2-6/WTpooled	1.09926	0.531
IL7-5/WTpooled	1.01607
IL7-3/WTpooled	1.02597	1
IL12-4/WTpooled	0.92769	1
IL1-4/WTpooled	1.0559
WT/WTpooled	1.00298	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	0.92539	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05903	0.921
DC3000/delta hrp 6h	1.09852	1
DC3000/delta hrp 12h	1.19447	1
DC3000/delta hrp 24h	0.65695	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61571	0.036
DC3000 delta B/DC3000 delta AB	0.50847	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08114	1
Exp 36h	0.73945	0.539
Exp 60h	0.51734	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97371	1
Var 0h	2.48883	0.936
Var 12h I row2-row1	0.76337	0.335
Var 12h NI row2-row1	1.01481	1
Var 36h I row2-row1	0.98761	1
Var 36h NI row2-row1	1.45833	0.482
Var 60h I row2-row1	1.07031	0.543
Var 60h NI row2-row1	1.03935	1
Time course 0hI-0hNI	0.99459	1
Time course 12hI-12hNI	0.99079	0.968
Time course 36hI-36hNI	0.93577	0.169
Time course 60hI-60hNI	0.29134	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)	1.01639	1
transgenic ySAMdc/azygous control (breaker)	1.90054	0.172
transgenic ySAMdc/azygous control (red)	1.20338	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.62868	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.45166	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.91066	0.083
Manapal/WT (break)	5.38097	0.123
Manapal/WT (red)	2.14504	0.222