Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73116	0.238
27DAP/17DAP	1.38212	0.749
39DAP/27DAP	1.38504	0.447
41DAP/39DAP	0.89064	0.483
42DAP/41DAP	2.57787	0.019
43DAP/42DAP	1.2576	0.321
47DAP/43DAP	0.47637	0.049
52DAP/47DAP	1.16404	0.804
57DAP/52DAP	1.16798	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80474	0.071
17DAP/reference	0.66485	0.007
27DAP/reference	0.79742	0.078
39DAP/reference	0.74636	0.018
41DAP/reference	0.65371	0.018
42DAP/reference	0.9558	0.211
43DAP/reference	1.21309	0.01
47DAP/reference	0.98166	0.473
52DAP/reference	0.99612	0.598
57DAP/reference	0.96337	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65174	0.066
27DAP/17DAP	0.54605	0.121
39DAP/27DAP	1.49659	0.15
41DAP/39DAP	1.2185	0.417
42DAP/41DAP	1.29411	0.025
43DAP/42DAP	1.04106	0.478
47DAP/43DAP	1.35636	0.051
52DAP/47DAP	0.75295	0.192
57DAP/52DAP	1.50623	0.079
57DAP/7DAP	1.60769	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02541	0.876
17DAP/reference	1.14479	0.297
27DAP/reference	1.05103	0.974
39DAP/reference	1.13059	0.267
41DAP/reference	1.00414	0.646
42DAP/reference	1.10628	0.174
43DAP/reference	1.254	0.06
47DAP/reference	1.16792	0.259
52DAP/reference	1.11072	0.139
57DAP/reference	1.02747	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84041	0.124
17DAP/reference	0.65479	0.005
27DAP/reference	0.75684	0.033
39DAP/reference	0.72453	0.015
41DAP/reference	0.91521	0.16
42DAP/reference	0.7904	0.05
43DAP/reference	0.86233	0.191
47DAP/reference	0.8396	0.079
52DAP/reference	0.62605	0.005
57DAP/reference	0.83457	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90853	0.29
17DAP/reference	0.8742	0.308
27DAP/reference	0.90464	0.206
39DAP/reference	1.00093	0.819
41DAP/reference	0.9606	0.512
42DAP/reference	1.09855	0.45
43DAP/reference	1.52979	0.087
47DAP/reference	0.99117	0.558
52DAP/reference	0.98503	0.718
57DAP/reference	0.91455	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1654	0.916
26DAP/20DAP	1.56695	0.223
34DAP/26DAP	0.63239	0.152
51DAP/34DAP	0.95093	0.758
52DAP/51DAP	0.79647	0.151
53DAP/52DAP	0.94184	0.783
55DAP/53DAP	1.21808	0.703
57DAP/55DAP	0.90509	0.644
62DAP/57DAP	1.00498	1
68DAP/62DAP	1.23189	0.821
68DAP/14DAP	1.11423	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.25134	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27895	0.287
Mature Green Tomato/Ripe Tomato	0.37505	0.038
Immature Eggplant/Mature Eggplant	1.52847	0.051
Ripe Pepper/Ripe Tomato	1.4786	1
Mature Eggplant/Ripe Tomato	2.82046	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.15861	0.455
1-1-2/M82	1.35664	1
12-2/M82	0.88656	0.955
12-4/M82	0.75577	0.619
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.62336
2-6/M82	1.44061
3-2/M82	0.99958	1
4-1-1/M82	0.49714
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.90216	0.268
5-3/M82	1.59176	0.572
6-2/M82	1.53647
6-3/M82	0.4828	0.387
7-1/M82	N/A	N/A
7-2/M82	1.54541	0.385
9-3-2/M82	1.91918	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.33943	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.70743	0.294
IL12-4/WTpooled	0.83847	0.581
IL1-4/WTpooled	0.98234
WT/WTpooled	1.03739	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	0.98564	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14361	0.75
DC3000/delta hrp 6h	0.9369	0.95
DC3000/delta hrp 12h	1.18986	1
DC3000/delta hrp 24h	1.0757	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.99289
DC3000 delta B/DC3000 delta AB	1.853	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09942	1
Exp 36h	1.38683	1
Exp 60h	1.36661	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04223	1
Var 0h	4.73898	0.98
Var 12h I row2-row1	1.28275	0.544
Var 12h NI row2-row1	0.85134	0.713
Var 36h I row2-row1	1.06084	1
Var 36h NI row2-row1	0.76479	0.482
Var 60h I row2-row1	1.24046	1
Var 60h NI row2-row1	0.79422	0.932
Time course 0hI-0hNI	1.18548	0.413
Time course 12hI-12hNI	1.22704	0.611
Time course 36hI-36hNI	2.32269	0.005
Time course 60hI-60hNI	7.0628	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)	0.78145	0.309
transgenic ySAMdc/azygous control (breaker)	3.32408	0.166
transgenic ySAMdc/azygous control (red)	0.62836	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.30324	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42719	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.14419	0.096
Manapal/WT (break)	1.56456	1
Manapal/WT (red)	1.527	0.222