Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00792	0.911
27DAP/17DAP	1.58736	0.521
39DAP/27DAP	1.389	0.181
41DAP/39DAP	0.88205	0.501
42DAP/41DAP	1.06809	0.941
43DAP/42DAP	1.00115	0.932
47DAP/43DAP	0.87747	0.599
52DAP/47DAP	0.83081	0.607
57DAP/52DAP	1.24084	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18575	0.059
17DAP/reference	1.16807	0.041
27DAP/reference	1.00486	1
39DAP/reference	1.10584	0.14
41DAP/reference	1.2713	0.122
42DAP/reference	1.12647	0.119
43DAP/reference	1.12434	0.445
47DAP/reference	1.16205	0.016
52DAP/reference	0.78517	0.019
57DAP/reference	0.9451	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30033	0.151
27DAP/17DAP	1.06734	0.915
39DAP/27DAP	1.27346	0.496
41DAP/39DAP	0.96644	0.934
42DAP/41DAP	1.05453	0.861
43DAP/42DAP	1.09784	0.297
47DAP/43DAP	0.96667	0.823
52DAP/47DAP	0.81075	0.23
57DAP/52DAP	0.97717	0.789
57DAP/7DAP	1.3002	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52034	0.027
17DAP/reference	1.56201	0.006
27DAP/reference	1.51035	0.014
39DAP/reference	1.42637	0.009
41DAP/reference	1.2533	0.101
42DAP/reference	1.29262	0.037
43DAP/reference	1.29654	0.022
47DAP/reference	1.44529	0.015
52DAP/reference	1.32213	0.021
57DAP/reference	1.41536	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16367	0.19
17DAP/reference	1.37495	0.008
27DAP/reference	1.2501	0.04
39DAP/reference	0.98506	0.539
41DAP/reference	0.97393	0.432
42DAP/reference	1.00966	1
43DAP/reference	1.06023	1
47DAP/reference	1.19298	0.074
52DAP/reference	1.05748	1
57DAP/reference	1.04561	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45694	0.025
17DAP/reference	1.18622	0.129
27DAP/reference	1.26596	0.078
39DAP/reference	1.35911	0.038
41DAP/reference	1.14328	0.439
42DAP/reference	1.03681	1
43DAP/reference	1.08039	0.655
47DAP/reference	0.99723	0.708
52DAP/reference	1.72913	0.035
57DAP/reference	0.90004	0.217

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94603	1
26DAP/20DAP	2.76793	0.093
34DAP/26DAP	1.61355	0.19
51DAP/34DAP	0.80783	0.587
52DAP/51DAP	0.89681	1
53DAP/52DAP	0.88282	0.631
55DAP/53DAP	0.64124	0.024
57DAP/55DAP	0.84724	0.351
62DAP/57DAP	1.37976	0.723
68DAP/62DAP	0.82957	0.641
68DAP/14DAP	0.73885	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60024	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59946	0.181
Mature Green Tomato/Ripe Tomato	1.22382	0.752
Immature Eggplant/Mature Eggplant	1.21717	0.081
Ripe Pepper/Ripe Tomato	0.66456	0.224
Mature Eggplant/Ripe Tomato	0.7852	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02657	1
1-1-2/M82	1.06719	1
12-2/M82	0.70857	0.862
12-4/M82	1.03314	1
1-3/M82	1.38932	0.479
2-1-1/M82	1.21127	0.457
2-1/M82	N/A	N/A
2-6/M82	0.93381
3-2/M82	N/A	N/A
4-1-1/M82	1.15471
4-1/M82	0.93408
4-3-2/M82	1.34183	1
4-3/M82	1.22945	1
5-3/M82	1.15992	1
6-2/M82	1.32032	1
6-3/M82	0.83591
7-1/M82	1.04121
7-2/M82	1.0838	0.385
9-3-2/M82	1.33409	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.83382	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.4489	1
IL12-4/WTpooled	0.99639	1
IL1-4/WTpooled	1.05147
WT/WTpooled	1.00491	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	1.84806	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00111	1
DC3000/delta hrp 6h	0.97001	0.95
DC3000/delta hrp 12h	0.97072	1
DC3000/delta hrp 24h	1.49775	0.074

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21299	0.045
DC3000 delta B/DC3000 delta AB	1.32112	0.139

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75395	1
Exp 36h	1.10671	0.489
Exp 60h	1.04048	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00777	1
Var 0h	0.421	0.332
Var 12h I row2-row1	0.81929	0.363
Var 12h NI row2-row1	1.46367	0.281
Var 36h I row2-row1	0.93983	1
Var 36h NI row2-row1	0.64427	0.478
Var 60h I row2-row1	0.66588	0.285
Var 60h NI row2-row1	0.69082	0.335
Time course 0hI-0hNI	1.05799	0.852
Time course 12hI-12hNI	1.14165	0.445
Time course 36hI-36hNI	2.14976	0.005
Time course 60hI-60hNI	13.5014	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)	0.95708	0.32
transgenic ySAMdc/azygous control (breaker)	1.03268	1
transgenic ySAMdc/azygous control (red)	1.02696	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0016	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64195	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76833	0.172
Manapal/WT (break)	0.85131	0.299
Manapal/WT (red)	1.28073	0.222