Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.12.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11837	0.63
27DAP/17DAP	0.85667	0.63
39DAP/27DAP	1.57993	0.501
41DAP/39DAP	0.46054	0.042
42DAP/41DAP	1.51939	0.777
43DAP/42DAP	1.45358	0.382
47DAP/43DAP	1.45292	0.239
52DAP/47DAP	0.67453	0.287
57DAP/52DAP	0.73452	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1296	0.814
17DAP/reference	1.39271	0.442
27DAP/reference	2.61772	0.009
39DAP/reference	1.23561	0.497
41DAP/reference	0.899	0.341
42DAP/reference	1.44263	0.001
43DAP/reference	1.54236	0.011
47DAP/reference	1.65437	0.001
52DAP/reference	1.07627	1
57DAP/reference	1.15951	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82708	0.036
27DAP/17DAP	0.8931	0.475
39DAP/27DAP	0.64824	0.028
41DAP/39DAP	0.92987	0.68
42DAP/41DAP	1.07118	0.872
43DAP/42DAP	0.9784	0.801
47DAP/43DAP	0.87143	0.075
52DAP/47DAP	0.80702	0.103
57DAP/52DAP	0.88059	0.494
57DAP/7DAP	0.43292	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34649	0.037
17DAP/reference	1.13007	0.059
27DAP/reference	1.39276	0.03
39DAP/reference	1.46651	0.016
41DAP/reference	0.89434	0.107
42DAP/reference	1.10403	0.686
43DAP/reference	1.27527	0.041
47DAP/reference	1.3041	0.06
52DAP/reference	1.3284	0.139
57DAP/reference	1.44883	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66576	0.022
17DAP/reference	1.00185	0.693
27DAP/reference	1.30207	0.153
39DAP/reference	1.27688	0.571
41DAP/reference	1.18028	0.362
42DAP/reference	1.12731	0.324
43DAP/reference	0.47583	0.005
47DAP/reference	0.84231	0.027
52DAP/reference	0.58557	0.004
57DAP/reference	0.45232	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.90754	0.016
17DAP/reference	1.46097	0.146
27DAP/reference	2.21003	0.014
39DAP/reference	2.02661	0.006
41DAP/reference	1.5576	0.007
42DAP/reference	2.17447	0.011
43DAP/reference	3.1544	0.006
47DAP/reference	3.03839	0.006
52DAP/reference	1.85877	0.048
57DAP/reference	8.72567	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.61211	0.916
26DAP/20DAP	0.96654	1
34DAP/26DAP	1.239	1
51DAP/34DAP	0.54888	0.054
52DAP/51DAP	0.87103	1
53DAP/52DAP	0.72673	0.049
55DAP/53DAP	0.73755	0.023
57DAP/55DAP	1.57252	0.626
62DAP/57DAP	0.94799	0.871
68DAP/62DAP	0.93962	0.747
68DAP/14DAP	0.70368	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64373	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87704	0.377
Mature Green Tomato/Ripe Tomato	2.10854	0.017
Immature Eggplant/Mature Eggplant	0.55429	0.062
Ripe Pepper/Ripe Tomato	1.34982	1
Mature Eggplant/Ripe Tomato	1.38758	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.32259	0.877
1-1-2/M82	1.66672	1
12-2/M82	0.93734	0.955
12-4/M82	2.43992	1
1-3/M82	3.63086	0.248
2-1-1/M82	0.71736	0.465
2-1/M82	0.66699	0.322
2-6/M82	1.61058	0.355
3-2/M82	0.84732	1
4-1-1/M82	1.33219	1
4-1/M82	2.44863	1
4-3-2/M82	1.55461	0.284
4-3/M82	0.97847	1
5-3/M82	0.94144	1
6-2/M82	1.74564	0.253
6-3/M82	0.88921	1
7-1/M82	1.19052	0.925
7-2/M82	1.9369	0.291
9-3-2/M82	1.74362	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11774	0.277
IL2-6/WTpooled	1.02231	1
IL7-5/WTpooled	0.97979	1
IL7-3/WTpooled	0.98854	1
IL12-4/WTpooled	1.0062	1
IL1-4/WTpooled	0.91907	0.834
WT/WTpooled	1.03056	0.957

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	0.95905	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98072	1
DC3000/delta hrp 6h	0.98722	0.95
DC3000/delta hrp 12h	1.28736	1
DC3000/delta hrp 24h	1.02176	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7595	0.026
DC3000 delta B/DC3000 delta AB	0.76841	0.036

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21042	1
Exp 36h	0.91324	0.82
Exp 60h	1.0341	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01727	1
Var 0h	0.52567	0.936
Var 12h I row2-row1	0.96826	0.77
Var 12h NI row2-row1	0.95186	0.82
Var 36h I row2-row1	0.89005	1
Var 36h NI row2-row1	1.05453	1
Var 60h I row2-row1	1.00423	1
Var 60h NI row2-row1	0.9698	1
Time course 0hI-0hNI	0.99882	1
Time course 12hI-12hNI	0.9837	0.909
Time course 36hI-36hNI	1.0098	0.908
Time course 60hI-60hNI	0.48553	0.011

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)	0.98619	0.789
transgenic ySAMdc/azygous control (breaker)	1.28363	0.248
transgenic ySAMdc/azygous control (red)	2.50773	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	2.03113	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02341	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.07999	0.096
Manapal/WT (break)	1.6495	0.381
Manapal/WT (red)	3.32917	0.142