Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74352	0.09
27DAP/17DAP	1.32057	0.781
39DAP/27DAP	1.26112	0.444
41DAP/39DAP	0.75331	0.225
42DAP/41DAP	1.01664	1
43DAP/42DAP	0.68353	0.454
47DAP/43DAP	1.12028	0.873
52DAP/47DAP	1.69289	0.498
57DAP/52DAP	0.93351	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33294	0.04
17DAP/reference	1.07123	0.185
27DAP/reference	0.97934	0.654
39DAP/reference	1.04265	0.57
41DAP/reference	1.1842	0.038
42DAP/reference	1.06817	0.287
43DAP/reference	0.95427	0.48
47DAP/reference	1.13739	0.154
52DAP/reference	1.01414	1
57DAP/reference	1.10886	0.344

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82251	0.148
27DAP/17DAP	1.05275	0.928
39DAP/27DAP	0.78479	0.156
41DAP/39DAP	0.95052	0.849
42DAP/41DAP	1.11692	0.622
43DAP/42DAP	0.96693	0.751
47DAP/43DAP	0.99829	0.99
52DAP/47DAP	0.85819	0.202
57DAP/52DAP	0.8935	0.473
57DAP/7DAP	0.60707	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87756	0.168
17DAP/reference	1.03832	0.822
27DAP/reference	1.01027	0.8
39DAP/reference	0.86778	0.083
41DAP/reference	0.85846	0.054
42DAP/reference	0.90525	0.16
43DAP/reference	0.90261	0.151
47DAP/reference	0.98811	0.671
52DAP/reference	0.87367	0.049
57DAP/reference	0.78612	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23279	0.175
17DAP/reference	1.34766	0.011
27DAP/reference	1.33063	0.046
39DAP/reference	1.10681	0.67
41DAP/reference	1.04557	1
42DAP/reference	1.18381	0.324
43DAP/reference	1.47757	0.033
47DAP/reference	1.15138	0.092
52DAP/reference	1.03894	0.667
57DAP/reference	1.41283	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97728	0.566
17DAP/reference	1.08392	0.551
27DAP/reference	1.03029	0.871
39DAP/reference	1.03166	0.733
41DAP/reference	0.94936	0.417
42DAP/reference	0.96145	0.552
43DAP/reference	1.12511	0.474
47DAP/reference	0.96673	0.478
52DAP/reference	0.86006	0.247
57DAP/reference	1.11946	0.354

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30842	0.966
26DAP/20DAP	1.07085	0.875
34DAP/26DAP	0.90259	0.256
51DAP/34DAP	1.07269	0.84
52DAP/51DAP	0.88787	1
53DAP/52DAP	0.74165	0.065
55DAP/53DAP	0.62359	0.026
57DAP/55DAP	0.85866	0.496
62DAP/57DAP	1.07453	0.902
68DAP/62DAP	0.98687	0.834
68DAP/14DAP	0.75073	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71986	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.2821	0.058
Mature Green Tomato/Ripe Tomato	1.48392	0.134
Immature Eggplant/Mature Eggplant	0.78487	0.084
Ripe Pepper/Ripe Tomato	0.6881	0.224
Mature Eggplant/Ripe Tomato	2.38425	0.26

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	0.96339	1
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	0.59189
4-3-2/M82	0.84545
4-3/M82	N/A	N/A
5-3/M82	0.93624	1
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	0.88909

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.0387	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85719	0.418
IL12-4/WTpooled	1.05581	0.737
IL1-4/WTpooled	1.16132	1
WT/WTpooled	0.99282	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	1.01878	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10055	0.921
DC3000/delta hrp 6h	0.95999	0.95
DC3000/delta hrp 12h	1.06024	1
DC3000/delta hrp 24h	0.86931	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95051	0.765
DC3000 delta B/DC3000 delta AB	0.8682	0.279

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84656	1
Exp 36h	1.12833	1
Exp 60h	0.94438	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00424	1
Var 0h	0.37766	1
Var 12h I row2-row1	1.16623	0.473
Var 12h NI row2-row1	1.21074	0.281
Var 36h I row2-row1	0.82598	1
Var 36h NI row2-row1	1.18518	1
Var 60h I row2-row1	0.85064	0.285
Var 60h NI row2-row1	1.02242	1
Time course 0hI-0hNI	1.02487	0.852
Time course 12hI-12hNI	0.92042	0.206
Time course 36hI-36hNI	0.93479	0.211
Time course 60hI-60hNI	1.08654	0.495

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)	0.984	0.862
transgenic ySAMdc/azygous control (breaker)	0.86216	0.173
transgenic ySAMdc/azygous control (red)	1.26059	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91846	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.41292	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07722	1
Manapal/WT (break)	1.98783	0.183
Manapal/WT (red)	1.3895	0.137