Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.4.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84733	0.297
27DAP/17DAP	1.03448	0.902
39DAP/27DAP	1.68531	0.068
41DAP/39DAP	0.68642	0.103
42DAP/41DAP	1.09702	1
43DAP/42DAP	1.19608	1
47DAP/43DAP	0.61126	0.084
52DAP/47DAP	1.17245	0.946
57DAP/52DAP	1.25022	0.806

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48489	0.008
17DAP/reference	0.93486	0.342
27DAP/reference	0.91434	0.327
39DAP/reference	0.85007	0.267
41DAP/reference	0.78587	0.039
42DAP/reference	1.45177	0.001
43DAP/reference	1.15527	0.133
47DAP/reference	1.00189	0.636
52DAP/reference	0.83153	0.125
57DAP/reference	1.03253	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9109	0.238
27DAP/17DAP	1.011	1
39DAP/27DAP	0.89266	0.239
41DAP/39DAP	1.41025	0.14
42DAP/41DAP	0.99591	0.864
43DAP/42DAP	0.99782	1
47DAP/43DAP	0.97066	0.855
52DAP/47DAP	0.80681	0.096
57DAP/52DAP	1.02026	0.925
57DAP/7DAP	1.01173	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.35733	0.024
17DAP/reference	1.48677	0.006
27DAP/reference	1.71802	0.006
39DAP/reference	1.49128	0.006
41DAP/reference	1.99689	0.009
42DAP/reference	2.02619	0.007
43DAP/reference	2.35601	0.006
47DAP/reference	1.81977	0.014
52DAP/reference	2.46726	0.007
57DAP/reference	1.65927	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31006	0.103
17DAP/reference	1.0849	0.599
27DAP/reference	1.85798	0.013
39DAP/reference	1.73584	0.021
41DAP/reference	1.40484	0.055
42DAP/reference	1.58441	0.04
43DAP/reference	1.18607	0.526
47DAP/reference	1.33356	0.069
52DAP/reference	0.85546	0.111
57DAP/reference	0.87402	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.62163	0.017
17DAP/reference	1.09845	0.456
27DAP/reference	1.4192	0.131
39DAP/reference	1.76001	0.006
41DAP/reference	1.46085	0.011
42DAP/reference	2.78786	0.012
43DAP/reference	2.90243	0.008
47DAP/reference	0.91462	0.224
52DAP/reference	1.98406	0.09
57DAP/reference	1.22807	0.175

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00925	1
26DAP/20DAP	1.31448	0.587
34DAP/26DAP	0.84087	0.419
51DAP/34DAP	1.51419	0.108
52DAP/51DAP	0.66401	0.151
53DAP/52DAP	1.10131	0.594
55DAP/53DAP	0.68651	0.102
57DAP/55DAP	1.20946	0.407
62DAP/57DAP	1.07407	0.868
68DAP/62DAP	1.01097	0.939
68DAP/14DAP	1.11847	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.51145	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59987	0.127
Mature Green Tomato/Ripe Tomato	1.31896	0.149
Immature Eggplant/Mature Eggplant	1.04858	0.3
Ripe Pepper/Ripe Tomato	1.62807	0.256
Mature Eggplant/Ripe Tomato	0.71839	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.69607	0.525
1-1-2/M82	0.77988
12-2/M82	0.9127	0.955
12-4/M82	1.02451	1
1-3/M82	2.04739	0.479
2-1-1/M82	0.90605	0.784
2-1/M82	0.81408	0.345
2-6/M82	0.90131	1
3-2/M82	0.85739	0.752
4-1-1/M82	0.7924	1
4-1/M82	0.61713
4-3-2/M82	1.08233	1
4-3/M82	1.01656	1
5-3/M82	1.16825	0.572
6-2/M82	1.67624	0.235
6-3/M82	1.22114	1
7-1/M82	1.0025	1
7-2/M82	1.24273	0.385
9-3-2/M82	1.12988	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.88436	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.16704
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.82605	0.71
IL1-4/WTpooled	1.05195
WT/WTpooled	1.01438	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	1.21521	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96537	1
DC3000/delta hrp 6h	0.84387	0.95
DC3000/delta hrp 12h	1.14036	1
DC3000/delta hrp 24h	0.94635	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.1025	0.472

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16529	1
Exp 36h	1.32111	1
Exp 60h	1.32836	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.88774	0.332
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.17713
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.04983	0.326
transgenic ySAMdc/azygous control (breaker)	0.74619	0.15
transgenic ySAMdc/azygous control (red)	0.7958	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11049	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71513	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8563	1
Manapal/WT (break)	0.97945	1
Manapal/WT (red)	1.16135	0.413