Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9331	0.627
27DAP/17DAP	1.29694	0.784
39DAP/27DAP	1.22363	0.593
41DAP/39DAP	1.05365	0.715
42DAP/41DAP	1.21573	0.868
43DAP/42DAP	1.04317	1
47DAP/43DAP	1.07288	0.943
52DAP/47DAP	0.93008	0.72
57DAP/52DAP	1.06683	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92337	0.254
17DAP/reference	0.99394	0.819
27DAP/reference	1.01243	0.794
39DAP/reference	0.96469	0.651
41DAP/reference	0.92626	0.049
42DAP/reference	0.97152	0.305
43DAP/reference	1.0398	0.518
47DAP/reference	1.04406	0.264
52DAP/reference	1.02226	0.951
57DAP/reference	1.0083	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01204	1
27DAP/17DAP	0.99543	0.943
39DAP/27DAP	1.02116	0.707
41DAP/39DAP	0.95448	0.91
42DAP/41DAP	1.02933	0.872
43DAP/42DAP	1.01932	0.788
47DAP/43DAP	1.00262	1
52DAP/47DAP	0.98661	0.913
57DAP/52DAP	0.98501	0.742
57DAP/7DAP	1.0094	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.942	0.095
17DAP/reference	0.80509	0.012
27DAP/reference	0.79301	0.011
39DAP/reference	0.92889	0.073
41DAP/reference	0.96232	0.469
42DAP/reference	1.02635	0.889
43DAP/reference	0.94418	0.192
47DAP/reference	1.05067	0.776
52DAP/reference	0.80204	0.022
57DAP/reference	0.81736	0.05

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94894	0.441
17DAP/reference	0.90389	0.036
27DAP/reference	0.93035	0.108
39DAP/reference	0.93405	0.129
41DAP/reference	0.8709	0.041
42DAP/reference	0.94591	0.212
43DAP/reference	0.96354	0.438
47DAP/reference	0.94895	0.097
52DAP/reference	0.91775	0.04
57DAP/reference	0.86351	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85785	0.05
17DAP/reference	0.89908	0.243
27DAP/reference	0.76189	0.03
39DAP/reference	0.92713	0.028
41DAP/reference	0.84866	0.018
42DAP/reference	1.1088	0.272
43DAP/reference	1.06095	0.547
47DAP/reference	1.08587	0.324
52DAP/reference	1.15472	0.312
57DAP/reference	0.96012	0.424

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01443	0.966
26DAP/20DAP	0.99249	1
34DAP/26DAP	1.05563	0.819
51DAP/34DAP	1.1031	0.164
52DAP/51DAP	0.94435	1
53DAP/52DAP	1.026	0.845
55DAP/53DAP	0.94646	0.592
57DAP/55DAP	1.08704	0.626
62DAP/57DAP	1.10297	0.723
68DAP/62DAP	1.13291	0.689
68DAP/14DAP	1.02622	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29175	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.49467	0.094
Mature Green Tomato/Ripe Tomato	0.78009	0.086
Immature Eggplant/Mature Eggplant	0.65863	0.065
Ripe Pepper/Ripe Tomato	0.73344	0.224
Mature Eggplant/Ripe Tomato	0.65268	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95277	0.944
1-1-2/M82	0.94396	0.667
12-2/M82	0.94239	0.955
12-4/M82	1.08805	1
1-3/M82	1.12748	1
2-1-1/M82	0.99618	1
2-1/M82	1.03263	1
2-6/M82	0.97707	1
3-2/M82	1.01619	1
4-1-1/M82	0.98543	1
4-1/M82	1.38539	0.853
4-3-2/M82	1.02355	1
4-3/M82	0.94326	0.72
5-3/M82	0.95233	1
6-2/M82	1.00002	1
6-3/M82	0.97345	1
7-1/M82	1.00094	1
7-2/M82	0.90826	0.578
9-3-2/M82	1.2829	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96536	1
IL7-5/WTpooled	0.10722
IL7-3/WTpooled	0.83657	0.298
IL12-4/WTpooled	0.87346	1
IL1-4/WTpooled	1.05881	1
WT/WTpooled	1.04122	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	1.23328	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99809	1
DC3000/delta hrp 6h	1.17416	1
DC3000/delta hrp 12h	1.02364	1
DC3000/delta hrp 24h	1.25762	0.158

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17583	0.042
DC3000 delta B/DC3000 delta AB	1.22867	0.142

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23108	1
Exp 36h	1.86263	0.693
Exp 60h	1.76992	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.019	1
Var 0h	0.96998	1
Var 12h I row2-row1	1.02012	1
Var 12h NI row2-row1	0.93891	0.403
Var 36h I row2-row1	0.96507	1
Var 36h NI row2-row1	0.94875	0.791
Var 60h I row2-row1	0.98371	0.952
Var 60h NI row2-row1	1.09393	0.904
Time course 0hI-0hNI	1.06477	0.833
Time course 12hI-12hNI	1.14898	0.26
Time course 36hI-36hNI	1.08777	0.58
Time course 60hI-60hNI	1.87951	0.008

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)	0.97748	0.789
transgenic ySAMdc/azygous control (breaker)	1.02783	1
transgenic ySAMdc/azygous control (red)	1.1453	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07986	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49672	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92563	1
Manapal/WT (break)	1.0113	1
Manapal/WT (red)	0.86782	0.242