Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.5.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19739	0.325
27DAP/17DAP	0.7866	0.326
39DAP/27DAP	1.07939	0.876
41DAP/39DAP	0.7825	0.242
42DAP/41DAP	1.03873	1
43DAP/42DAP	1.08566	1
47DAP/43DAP	0.89557	0.634
52DAP/47DAP	1.03174	0.916
57DAP/52DAP	1.03085	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96278	0.489
17DAP/reference	1.19681	0.024
27DAP/reference	1.08724	0.211
39DAP/reference	1.11463	0.013
41DAP/reference	1.2534	0.085
42DAP/reference	0.88361	0.023
43DAP/reference	1.13696	0.053
47DAP/reference	0.95161	0.3
52DAP/reference	0.8744	0.195
57DAP/reference	0.81005	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16974	0.581
27DAP/17DAP	1.10217	0.639
39DAP/27DAP	0.67589	0.031
41DAP/39DAP	0.94781	0.885
42DAP/41DAP	1.09122	0.719
43DAP/42DAP	0.72369	0.022
47DAP/43DAP	1.08395	0.805
52DAP/47DAP	0.97833	0.917
57DAP/52DAP	0.88627	0.476
57DAP/7DAP	0.40814	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04055	1
17DAP/reference	1.08266	0.822
27DAP/reference	0.95078	0.325
39DAP/reference	1.05944	0.705
41DAP/reference	1.06496	0.375
42DAP/reference	0.89527	0.32
43DAP/reference	1.25674	0.118
47DAP/reference	1.04148	0.854
52DAP/reference	1.13043	0.149
57DAP/reference	1.15828	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30607	0.079
17DAP/reference	1.30168	0.066
27DAP/reference	1.11554	0.195
39DAP/reference	1.06985	0.824
41DAP/reference	0.91306	0.173
42DAP/reference	0.94687	0.212
43DAP/reference	1.22634	0.401
47DAP/reference	0.99275	0.643
52DAP/reference	1.18163	0.074
57DAP/reference	1.1995	0.025

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02433	1
17DAP/reference	1.11104	0.689
27DAP/reference	0.85094	0.092
39DAP/reference	0.96316	0.544
41DAP/reference	0.90907	0.512
42DAP/reference	0.76313	0.361
43DAP/reference	1.06662	0.961
47DAP/reference	0.98809	0.593
52DAP/reference	1.03148	0.928
57DAP/reference	0.82404	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09914	0.966
26DAP/20DAP	0.91784	1
34DAP/26DAP	1.53982	0.819
51DAP/34DAP	1.11195	0.719
52DAP/51DAP	0.61688	0.151
53DAP/52DAP	1.38718	0.125
55DAP/53DAP	0.94297	0.663
57DAP/55DAP	1.28924	0.764
62DAP/57DAP	0.79235	0.466
68DAP/62DAP	1.2124	1
68DAP/14DAP	0.96926	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55169	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06684	0.666
Mature Green Tomato/Ripe Tomato	1.76796	0.015
Immature Eggplant/Mature Eggplant	0.63763	0.077
Ripe Pepper/Ripe Tomato	1.07138	1
Mature Eggplant/Ripe Tomato	0.70071	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.66168
1-1-2/M82	0.94553	0.804
12-2/M82	N/A	N/A
12-4/M82	0.96014	1
1-3/M82	N/A	N/A
2-1-1/M82	0.58279
2-1/M82	N/A	N/A
2-6/M82	0.96138	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.71866
4-3-2/M82	0.89374
4-3/M82	0.84099	0.611
5-3/M82	0.85365	1
6-2/M82	1.10152	1
6-3/M82	1.02936	1
7-1/M82	1.03582	1
7-2/M82	1.05966
9-3-2/M82	1.23631

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.83918	0.395
IL7-5/WTpooled	1.42352
IL7-3/WTpooled	0.57102	0.31
IL12-4/WTpooled	1.36629	0.673
IL1-4/WTpooled	1.00228	1
WT/WTpooled	0.85135	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	1.1452	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93387	1
DC3000/delta hrp 6h	1.0809	1
DC3000/delta hrp 12h	1.04727	1
DC3000/delta hrp 24h	0.56596	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.48729	0.026
DC3000 delta B/DC3000 delta AB	0.51424	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24611	1
Exp 36h	0.70914	0.456
Exp 60h	0.6712	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01477	1
Var 0h	1.07404	1
Var 12h I row2-row1	0.69316	0.338
Var 12h NI row2-row1	0.82803	0.438
Var 36h I row2-row1	1.12407	1
Var 36h NI row2-row1	1.46444	0.253
Var 60h I row2-row1	0.80172
Var 60h NI row2-row1	1.06122	1
Time course 0hI-0hNI	0.93751	0.548
Time course 12hI-12hNI	0.92727	0.407
Time course 36hI-36hNI	0.80676	0.043
Time course 60hI-60hNI	0.17103	0.005

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)	0.99646	0.931
transgenic ySAMdc/azygous control (breaker)	0.88273	0.49
transgenic ySAMdc/azygous control (red)	1.11157	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96472	0.248

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9515	1
Manapal/WT (break)	1.21865	0.123
Manapal/WT (red)	1.04169	1