Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.4.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68266	0.073
27DAP/17DAP	0.85504	0.753
39DAP/27DAP	0.70401	0.265
41DAP/39DAP	1.67185	0.386
42DAP/41DAP	1.39583	0.66
43DAP/42DAP	1.02897	0.937
47DAP/43DAP	1.12346	0.702
52DAP/47DAP	1.02898	0.946
57DAP/52DAP	0.88905	0.879

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98849	0.645
17DAP/reference	0.89994	0.05
27DAP/reference	1.03819	0.771
39DAP/reference	1.15524	0.068
41DAP/reference	0.92617	0.341
42DAP/reference	0.96349	0.151
43DAP/reference	0.91908	0.148
47DAP/reference	1.0031	0.72
52DAP/reference	1.13087	0.134
57DAP/reference	1.12979	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06559	0.923
27DAP/17DAP	0.82191	0.446
39DAP/27DAP	1.09165	0.492
41DAP/39DAP	0.86051	0.696
42DAP/41DAP	1.57578	0.559
43DAP/42DAP	0.9639	0.774
47DAP/43DAP	1.01578	1
52DAP/47DAP	0.97591	0.925
57DAP/52DAP	1.17565	0.411
57DAP/7DAP	0.79796

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93736	0.146
17DAP/reference	1.15708	0.054
27DAP/reference	1.20303	0.16
39DAP/reference	1.19718	0.081
41DAP/reference	1.18769	0.057
42DAP/reference	1.14698	0.037
43DAP/reference	0.99368	0.637
47DAP/reference	0.98957	0.671
52DAP/reference	1.15097	0.229
57DAP/reference	1.25504	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00087	0.97
17DAP/reference	1.13038	0.459
27DAP/reference	0.92372	0.393
39DAP/reference	0.96491	0.509
41DAP/reference	0.88614	0.124
42DAP/reference	1.15415	0.195
43DAP/reference	1.32547	0.122
47DAP/reference	0.92303	0.126
52DAP/reference	1.00738	0.713
57DAP/reference	1.09031	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10752	0.588
17DAP/reference	1.02465	1
27DAP/reference	1.03331	0.672
39DAP/reference	1.01864	0.962
41DAP/reference	1.25627	0.015
42DAP/reference	1.04543	0.877
43DAP/reference	1.04046	0.617
47DAP/reference	1.01596	1
52DAP/reference	1.27272	0.301
57DAP/reference	1.04299	0.856

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30159	0.966
26DAP/20DAP	0.91921	1
34DAP/26DAP	1.1697	1
51DAP/34DAP	0.93678	0.785
52DAP/51DAP	0.87129	1
53DAP/52DAP	1.12717	0.895
55DAP/53DAP	0.6564	0.04
57DAP/55DAP	1.30978	0.935
62DAP/57DAP	0.8449	0.871
68DAP/62DAP	1.06382	0.926
68DAP/14DAP	0.81542	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20213	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.75455	0.217
Mature Green Tomato/Ripe Tomato	1.52419	0.077
Immature Eggplant/Mature Eggplant	1.38631	0.05
Ripe Pepper/Ripe Tomato	4.01476	0.258
Mature Eggplant/Ripe Tomato	1.57677	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14289	1
1-1-2/M82	1.07373	1
12-2/M82	N/A	N/A
12-4/M82	1.08864
1-3/M82	0.65039
2-1-1/M82	1.30882
2-1/M82	N/A	N/A
2-6/M82	0.91704
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.95408	0.395
6-2/M82	N/A	N/A
6-3/M82	1.06306
7-1/M82	N/A	N/A
7-2/M82	0.84266	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66267	0.243
IL2-6/WTpooled	0.86373	1
IL7-5/WTpooled	1.23715	0.792
IL7-3/WTpooled	0.767	0.418
IL12-4/WTpooled	1.17423	0.532
IL1-4/WTpooled	0.90602	0.834
WT/WTpooled	0.89338	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	0.93107	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10964	0.894
DC3000/delta hrp 6h	1.05416	1
DC3000/delta hrp 12h	0.95164	1
DC3000/delta hrp 24h	1.08114	0.535

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.03025	1
Exp 60h	1.09007	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	N/A	N/A
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)	0.99983	1
transgenic ySAMdc/azygous control (breaker)	1.33602	0.248
transgenic ySAMdc/azygous control (red)	1.02774	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01494	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72434	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85632	1
Manapal/WT (break)	0.91831	1
Manapal/WT (red)	1.14542	1