Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.4.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07387	0.827
27DAP/17DAP	1.19654	0.872
39DAP/27DAP	1.03791	1
41DAP/39DAP	0.63052	0.066
42DAP/41DAP	1.51284	0.712
43DAP/42DAP	1.42264	0.864
47DAP/43DAP	1.21879	0.576
52DAP/47DAP	0.82249	0.54
57DAP/52DAP	1.33787	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97521	0.578
17DAP/reference	0.8129	0.097
27DAP/reference	1.14538	0.548
39DAP/reference	1.7956	0.019
41DAP/reference	1.61241	0.014
42DAP/reference	1.167	0.012
43DAP/reference	1.48149	0.008
47DAP/reference	2.04145	0.001
52DAP/reference	1.15243	0.141
57DAP/reference	1.33669	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40919	0.179
27DAP/17DAP	0.78806	0.227
39DAP/27DAP	1.12832	0.46
41DAP/39DAP	1.47419	0.497
42DAP/41DAP	0.93043	0.439
43DAP/42DAP	0.94135	0.293
47DAP/43DAP	0.93902	0.637
52DAP/47DAP	1.14217	0.598
57DAP/52DAP	0.52573	0.043
57DAP/7DAP	0.68002	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16512	0.209
17DAP/reference	1.02813	1
27DAP/reference	0.75842	0.058
39DAP/reference	1.45713	0.009
41DAP/reference	1.10088	0.109
42DAP/reference	1.17881	0.059
43DAP/reference	1.10313	0.457
47DAP/reference	1.17347	0.052
52DAP/reference	1.00247	0.802
57DAP/reference	1.07125	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87576	0.412
17DAP/reference	0.90258	0.347
27DAP/reference	0.68767	0.045
39DAP/reference	1.4102	0.019
41DAP/reference	1.06567	0.502
42DAP/reference	0.87797	0.067
43DAP/reference	0.76075	0.08
47DAP/reference	1.14388	0.133
52DAP/reference	1.01217	1
57DAP/reference	0.8081	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74705	0.055
17DAP/reference	0.6377	0.045
27DAP/reference	0.54887	0.029
39DAP/reference	0.73943	0.035
41DAP/reference	0.7392	0.019
42DAP/reference	0.85627	0.22
43DAP/reference	1.10051	0.452
47DAP/reference	1.04669	1
52DAP/reference	0.91359	0.368
57DAP/reference	1.15632	0.311

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04786	0.966
26DAP/20DAP	0.7069	0.317
34DAP/26DAP	0.99939	1
51DAP/34DAP	1.26856	0.215
52DAP/51DAP	0.69475	0.079
53DAP/52DAP	0.89589	0.631
55DAP/53DAP	0.77677	0.176
57DAP/55DAP	1.29327	0.543
62DAP/57DAP	1.3763	0.217
68DAP/62DAP	0.66909	0.245
68DAP/14DAP	0.73489	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.12868	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84714	0.312
Mature Green Tomato/Ripe Tomato	1.67573	0.016
Immature Eggplant/Mature Eggplant	1.06729	0.288
Ripe Pepper/Ripe Tomato	0.97558	1
Mature Eggplant/Ripe Tomato	0.91772	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.57024	0.574
1-1-2/M82	1.2876	0.977
12-2/M82	0.7604	0.678
12-4/M82	1.27018	1
1-3/M82	2.27681	0.479
2-1-1/M82	1.2592
2-1/M82	0.97126	1
2-6/M82	1.63668	0.395
3-2/M82	1.3092	0.717
4-1-1/M82	0.56265
4-1/M82	1.83502	1
4-3-2/M82	1.41935	0.508
4-3/M82	1.27807	0.268
5-3/M82	1.07786	1
6-2/M82	N/A	N/A
6-3/M82	0.53167	0.715
7-1/M82	0.81851	0.803
7-2/M82	1.18113	0.385
9-3-2/M82	1.86855	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.82941	1
IL1-4/WTpooled	0.90591
WT/WTpooled	1.18847

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	1.07293	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03041	1
DC3000/delta hrp 6h	1.27819	1
DC3000/delta hrp 12h	1.12455	1
DC3000/delta hrp 24h	1.01255	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.54159	0.05
DC3000 delta B/DC3000 delta AB	1.39567	0.114

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08656	1
Exp 36h	1.12654	1
Exp 60h	1.0155	1

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	0.87798	0.214
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
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)	0.75694	0.246
transgenic ySAMdc/azygous control (breaker)	0.97491	1
transgenic ySAMdc/azygous control (red)	0.9051	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11928	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86937	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44589	0.14
Manapal/WT (break)	1.04963	1
Manapal/WT (red)	0.81603	0.183