Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17583	0.561
27DAP/17DAP	0.89324	0.725
39DAP/27DAP	1.05197	1
41DAP/39DAP	1.17236	0.516
42DAP/41DAP	0.85608	1
43DAP/42DAP	1.20165	0.957
47DAP/43DAP	0.99341	0.913
52DAP/47DAP	1.24259	0.715
57DAP/52DAP	0.9771	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12944	0.544
17DAP/reference	1.30927	0.546
27DAP/reference	1.2523	0.049
39DAP/reference	0.9123	0.221
41DAP/reference	1.07995	0.265
42DAP/reference	1.17426	0.324
43DAP/reference	1.01372	0.84
47DAP/reference	1.1059	0.093
52DAP/reference	0.90238	0.35
57DAP/reference	1.26984	0.166

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.93686	0.63
27DAP/17DAP	0.80247	0.684
39DAP/27DAP	1.13768	0.672
41DAP/39DAP	0.97078	0.997
42DAP/41DAP	1.19153	0.783
43DAP/42DAP	1.18908	0.273
47DAP/43DAP	0.90664	0.554
52DAP/47DAP	0.79159	0.482
57DAP/52DAP	0.96479	0.601
57DAP/7DAP	1.87085	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65686	0.024
17DAP/reference	1.02567	0.896
27DAP/reference	0.7115	0.01
39DAP/reference	0.54271	0.015
41DAP/reference	0.58163	0.035
42DAP/reference	0.36244	0.01
43DAP/reference	0.33183	0.011
47DAP/reference	0.54596	0.101
52DAP/reference	0.45572	0.011
57DAP/reference	0.5162	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11648	1
17DAP/reference	0.93899	0.548
27DAP/reference	0.96536	0.519
39DAP/reference	0.96065	0.485
41DAP/reference	1.09148	0.96
42DAP/reference	0.88444	0.321
43DAP/reference	0.73966	0.236
47DAP/reference	0.98959	0.678
52DAP/reference	1.26554	0.528
57DAP/reference	0.91913	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.52743	0.015
17DAP/reference	2.10857	0.221
27DAP/reference	1.9297	0.017
39DAP/reference	1.62375	0.012
41DAP/reference	0.94327	0.293
42DAP/reference	0.61997	0.032
43DAP/reference	0.68284	0.025
47DAP/reference	1.1958	1
52DAP/reference	0.60086	0.066
57DAP/reference	1.19367	0.192

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2102	1
26DAP/20DAP	1.02775	1
34DAP/26DAP	1.63372	1
51DAP/34DAP	0.7903	0.286
52DAP/51DAP	0.95322	1
53DAP/52DAP	1.16859	0.935
55DAP/53DAP	0.79462	0.04
57DAP/55DAP	0.89482	0.601
62DAP/57DAP	0.93908	0.994
68DAP/62DAP	1.0115	0.939
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.34288	0.015

Experiment: Solanaceae fruit comparison

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

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	N/A	N/A
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	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02331	1
IL2-6/WTpooled	0.98196	1
IL7-5/WTpooled	1.21895	0.792
IL7-3/WTpooled	0.91849	0.418
IL12-4/WTpooled	0.84702	0.581
IL1-4/WTpooled	1.01844	1
WT/WTpooled	1.01222	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98061	1
DC3000/delta hrp 6h	0.98225	0.95
DC3000/delta hrp 12h	1.01353	1
DC3000/delta hrp 24h	0.42249	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42989	0.042
DC3000 delta B/DC3000 delta AB	1.27906	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97985	1
Exp 36h	0.54888	0.471
Exp 60h	0.38259	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00392
Var 0h	1.14807	0.782
Var 12h I row2-row1	0.8182	0.363
Var 12h NI row2-row1	0.65833	0.713
Var 36h I row2-row1	1.06932
Var 36h NI row2-row1	0.67501	1
Var 60h I row2-row1	1.06737	0.543
Var 60h NI row2-row1	0.99054	1
Time course 0hI-0hNI	0.99886	1
Time course 12hI-12hNI	0.92423	0.375
Time course 36hI-36hNI	0.92013	0.198
Time course 60hI-60hNI	0.42486	0.006

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)	0.89332	0.529
transgenic ySAMdc/azygous control (breaker)	0.82786	1
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.34439	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.0238	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12325	0.14
Manapal/WT (break)	0.9235	1
Manapal/WT (red)	N/A	N/A