Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.36702	0.014
27DAP/17DAP	0.46448	0.04
39DAP/27DAP	0.83738	0.549
41DAP/39DAP	0.57345	0.063
42DAP/41DAP	0.81158	1
43DAP/42DAP	1.28005	0.772
47DAP/43DAP	0.7808	0.35
52DAP/47DAP	1.32706	0.665
57DAP/52DAP	1.05518	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.56016	0.007
17DAP/reference	1.61825	0.017
27DAP/reference	2.0583	0.023
39DAP/reference	0.59167	0.019
41DAP/reference	0.53886	0.008
42DAP/reference	0.58803	0.001
43DAP/reference	0.39175	0.013
47DAP/reference	0.41928	0.001
52DAP/reference	0.38788	0.015
57DAP/reference	0.50805	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.24616	0.019
27DAP/17DAP	1.34954	0.04
39DAP/27DAP	0.55605	0.029
41DAP/39DAP	0.51401	0.026
42DAP/41DAP	1.05442	1
43DAP/42DAP	1.09937	0.746
47DAP/43DAP	1.77657	0.848
52DAP/47DAP	1.22439	0.779
57DAP/52DAP	1.03352	0.929
57DAP/7DAP	0.29222	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.63389	0.029
17DAP/reference	5.0322	0.006
27DAP/reference	6.08799	0.006
39DAP/reference	6.84887	0.005
41DAP/reference	6.4589	0.017
42DAP/reference	9.44347	0.006
43DAP/reference	10.7887	0.006
47DAP/reference	3.76808	0.885
52DAP/reference	8.48256	0.007
57DAP/reference	5.42228	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.78999	0.035
17DAP/reference	1.8655	0.007
27DAP/reference	1.00579	0.619
39DAP/reference	0.4254	0.008
41DAP/reference	0.56269	0.012
42DAP/reference	0.85997	0.212
43DAP/reference	0.62272	0.016
47DAP/reference	0.43433	0.01
52DAP/reference	0.47711	0.004
57DAP/reference	0.51219	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.8917	0.016
17DAP/reference	2.49596	0.179
27DAP/reference	5.09049	0.016
39DAP/reference	5.31714	0.019
41DAP/reference	4.5768	0.012
42DAP/reference	4.21662	0.171
43DAP/reference	3.78538	0.264
47DAP/reference	0.40515	0.006
52DAP/reference	4.45166	0.369
57DAP/reference	2.29106	0.661

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12628	1
26DAP/20DAP	1.35131	0.187
34DAP/26DAP	0.967	0.92
51DAP/34DAP	0.66075	0.069
52DAP/51DAP	0.74038	0.079
53DAP/52DAP	0.8029	0.173
55DAP/53DAP	0.62406	0.016
57DAP/55DAP	0.70036	0.08
62DAP/57DAP	0.89567	0.681
68DAP/62DAP	1.44765	0.124
68DAP/14DAP	1.34126	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.10981	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.98842	0.058
Mature Green Tomato/Ripe Tomato	18.7757	0.015
Immature Eggplant/Mature Eggplant	0.4303	0.057
Ripe Pepper/Ripe Tomato	138.624	0.256
Mature Eggplant/Ripe Tomato	596.528	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.00106
12-2/M82	N/A	N/A
12-4/M82	0.67179
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.72967
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88869
IL2-6/WTpooled	1.09548	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.92315	1
IL12-4/WTpooled	0.66991	0.543
IL1-4/WTpooled	1.30419	1
WT/WTpooled	0.91461	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	1.17454	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96998	0.734
DC3000/delta hrp 6h	0.84951	0.95
DC3000/delta hrp 12h	0.65737	1
DC3000/delta hrp 24h	0.65126	0.114

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.49849	0.023
DC3000 delta B/DC3000 delta AB	0.51984	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91772	1
Exp 36h	0.59686	0.406
Exp 60h	0.58696	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99378	1
Var 0h	0.97762	1
Var 12h I row2-row1	0.77861	0.338
Var 12h NI row2-row1	0.86619	0.494
Var 36h I row2-row1	1.01914	1
Var 36h NI row2-row1	1.19964	1
Var 60h I row2-row1	1.51614	0.562
Var 60h NI row2-row1	1.06451	0.904
Time course 0hI-0hNI	0.98757	0.979
Time course 12hI-12hNI	0.89604	0.347
Time course 36hI-36hNI	0.72664	0.023
Time course 60hI-60hNI	0.09024	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)	0.70395	0.32
transgenic ySAMdc/azygous control (breaker)	1.01987	1
transgenic ySAMdc/azygous control (red)	1.27736	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7181	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.13349	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.25331	0.307
Manapal/WT (break)	1.7081	1
Manapal/WT (red)	1.06341	1