Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99711	0.858
27DAP/17DAP	0.77037	0.345
39DAP/27DAP	1.33631	0.473
41DAP/39DAP	0.71321	0.092
42DAP/41DAP	0.9134	1
43DAP/42DAP	1.04007	1
47DAP/43DAP	0.9072	0.68
52DAP/47DAP	1.17871	0.662
57DAP/52DAP	1.10712	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1485	0.062
17DAP/reference	1.01557	0.696
27DAP/reference	0.97963	0.581
39DAP/reference	1.02727	0.664
41DAP/reference	0.97295	0.667
42DAP/reference	0.99219	0.484
43DAP/reference	0.9054	0.043
47DAP/reference	0.85769	0.011
52DAP/reference	0.85815	0.048
57DAP/reference	0.81456	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09165	0.508
27DAP/17DAP	1.03818	0.942
39DAP/27DAP	0.80411	0.134
41DAP/39DAP	1.12747	0.774
42DAP/41DAP	1.00363	1
43DAP/42DAP	0.76519	0.025
47DAP/43DAP	0.99939	0.99
52DAP/47DAP	0.98888	0.93
57DAP/52DAP	0.93906	0.56
57DAP/7DAP	0.63269	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24125	0.091
17DAP/reference	0.94138	0.072
27DAP/reference	0.98548	0.53
39DAP/reference	0.83353	0.023
41DAP/reference	0.78136	0.017
42DAP/reference	0.88181	0.012
43DAP/reference	0.72768	0.009
47DAP/reference	0.97525	0.671
52DAP/reference	0.77094	0.015
57DAP/reference	0.75589	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10241	0.172
17DAP/reference	1.15586	0.104
27DAP/reference	1.04562	1
39DAP/reference	1.03183	0.848
41DAP/reference	0.90642	0.074
42DAP/reference	0.99898	0.655
43DAP/reference	1.08102	0.146
47DAP/reference	0.9192	0.123
52DAP/reference	0.95086	0.28
57DAP/reference	0.9231	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38285	0.025
17DAP/reference	1.13686	0.179
27DAP/reference	0.88664	0.133
39DAP/reference	0.91332	0.111
41DAP/reference	1.11735	0.889
42DAP/reference	0.97981	0.671
43DAP/reference	0.84508	0.098
47DAP/reference	1.02757	0.934
52DAP/reference	0.79197	0.087
57DAP/reference	0.94197	0.402

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91908	1
26DAP/20DAP	1.14744	0.642
34DAP/26DAP	1.0413	1
51DAP/34DAP	1.25319	0.118
52DAP/51DAP	0.91724	1
53DAP/52DAP	0.94189
55DAP/53DAP	0.86469	0.056
57DAP/55DAP	1.12689	0.826
62DAP/57DAP	1.15086	0.303
68DAP/62DAP	0.76009	0.152
68DAP/14DAP	0.93783	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65305	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.97122	0.058
Mature Green Tomato/Ripe Tomato	2.71748	0.02
Immature Eggplant/Mature Eggplant	0.6011	0.063
Ripe Pepper/Ripe Tomato	4.32594	0.258
Mature Eggplant/Ripe Tomato	7.10381	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85166	0.402
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.98177	1
1-3/M82	N/A	N/A
2-1-1/M82	1.09567
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.72993
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	0.9404	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82719	1
IL2-6/WTpooled	0.79106	0.358
IL7-5/WTpooled	1.26443	0.792
IL7-3/WTpooled	1.06426	1
IL12-4/WTpooled	1.04333	1
IL1-4/WTpooled	1.0507	1
WT/WTpooled	0.90422	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	0.99719	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9904	1
DC3000/delta hrp 6h	1.03671	1
DC3000/delta hrp 12h	1.00672	1
DC3000/delta hrp 24h	0.63491	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.70979	0.023
DC3000 delta B/DC3000 delta AB	0.68324	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00736	1
Var 0h	1.20092	1
Var 12h I row2-row1	0.95132	0.77
Var 12h NI row2-row1	0.96993	0.627
Var 36h I row2-row1	1.00993	1
Var 36h NI row2-row1	1.41363	1
Var 60h I row2-row1	0.93127	0.952
Var 60h NI row2-row1	0.99994	1
Time course 0hI-0hNI	1.02841	0.63
Time course 12hI-12hNI	0.98381	0.87
Time course 36hI-36hNI	1.01162	0.799
Time course 60hI-60hNI	0.99589	1

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)	0.83151	0.297
transgenic ySAMdc/azygous control (breaker)	1.80177	0.248
transgenic ySAMdc/azygous control (red)	0.99162	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02806	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.82228	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.48093	0.083
Manapal/WT (break)	2.38367	0.123
Manapal/WT (red)	3.32025	0.133