Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.2.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92531	0.543
27DAP/17DAP	0.5407	0.063
39DAP/27DAP	0.89903	0.608
41DAP/39DAP	0.56795	0.06
42DAP/41DAP	1.0105	1
43DAP/42DAP	1.19703	0.714
47DAP/43DAP	1.02894	0.913
52DAP/47DAP	0.95713	0.859
57DAP/52DAP	1.28634	0.878

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54324	0.007
17DAP/reference	1.0069	0.819
27DAP/reference	1.24949	0.045
39DAP/reference	0.69894	0.011
41DAP/reference	0.65957	0.009
42DAP/reference	0.7991	0.013
43DAP/reference	0.88649	0.155
47DAP/reference	0.88622	0.161
52DAP/reference	1.18682	0.8
57DAP/reference	1.41405	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.35711	0.026
27DAP/17DAP	1.94366	0.023
39DAP/27DAP	0.46518	0.029
41DAP/39DAP	0.39777	0.017
42DAP/41DAP	1.25438	0.773
43DAP/42DAP	1.52468	0.028
47DAP/43DAP	0.76308	0.064
52DAP/47DAP	1.09986	0.826
57DAP/52DAP	1.03646	0.978
57DAP/7DAP	0.29864	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89657	0.361
17DAP/reference	0.88807	0.22
27DAP/reference	0.73645	0.088
39DAP/reference	1.29328	0.282
41DAP/reference	1.15965	0.475
42DAP/reference	0.92568	0.371
43DAP/reference	0.94378	0.351
47DAP/reference	0.75869	0.128
52DAP/reference	1.07605	0.832
57DAP/reference	1.11522	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26565	0.438
17DAP/reference	1.27205	0.203
27DAP/reference	1.09431	0.769
39DAP/reference	0.89448	0.189
41DAP/reference	0.94946	0.322
42DAP/reference	0.99436	0.655
43DAP/reference	0.54244	0.005
47DAP/reference	0.687	0.014
52DAP/reference	0.81602	0.037
57DAP/reference	0.6688	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26628	0.32
17DAP/reference	1.2937	0.248
27DAP/reference	1.24733	0.644
39DAP/reference	1.14688	0.889
41DAP/reference	1.07971	0.777
42DAP/reference	1.15028	0.566
43DAP/reference	1.15289	0.499
47DAP/reference	0.6288	0.006
52DAP/reference	1.01139	0.69
57DAP/reference	1.06025	0.581

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.79271	0.787
26DAP/20DAP	1.01035	1
34DAP/26DAP	0.71797	0.092
51DAP/34DAP	0.62131	0.077
52DAP/51DAP	1.03808	0.848
53DAP/52DAP	0.80093	0.083
55DAP/53DAP	0.60197	0.037
57DAP/55DAP	0.65606	0.057
62DAP/57DAP	1.31887	0.868
68DAP/62DAP	1.51836	0.06
68DAP/14DAP	0.76568	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.11864	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.58692	0.058
Mature Green Tomato/Ripe Tomato	5.23131	0.015
Immature Eggplant/Mature Eggplant	0.3	0.062
Ripe Pepper/Ripe Tomato	3.25753	1
Mature Eggplant/Ripe Tomato	7.1341	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98205	1
1-1-2/M82	0.87819
12-2/M82	1.00822
12-4/M82	0.997
1-3/M82	1.00456
2-1-1/M82	1.04314
2-1/M82	1.05977
2-6/M82	0.93464
3-2/M82	0.89206
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	0.90365	1
5-3/M82	1.00315	1
6-2/M82	N/A	N/A
6-3/M82	0.96207
7-1/M82	N/A	N/A
7-2/M82	1.08661	1
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	1.52285	0.46
IL7-5/WTpooled	2.20513
IL7-3/WTpooled	0.9785	1
IL12-4/WTpooled	0.90727	1
IL1-4/WTpooled	0.95906
WT/WTpooled	1.01028	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	1.08148	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0169	0.921
DC3000/delta hrp 6h	1.13807	1
DC3000/delta hrp 12h	0.86485	1
DC3000/delta hrp 24h	1.19104	0.062

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.3701	0.03
DC3000 delta B/DC3000 delta AB	0.41046	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92256	1
Exp 36h	0.66859	0.419
Exp 60h	0.54259	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01488	1
Var 0h	1.09726	0.421
Var 12h I row2-row1	0.98376	1
Var 12h NI row2-row1	0.96435	0.82
Var 36h I row2-row1	1.08223	0.908
Var 36h NI row2-row1	1.24992	1
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.99315	1
Time course 0hI-0hNI	1.02385	0.867
Time course 12hI-12hNI	1.00166	1
Time course 36hI-36hNI	0.87565	0.055
Time course 60hI-60hNI	0.11505	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)	0.7192	0.315
transgenic ySAMdc/azygous control (breaker)	1.82618	1
transgenic ySAMdc/azygous control (red)	1.04084	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.76503	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.53881	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.40479	0.307
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.71677	0.181