Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.57121	0.036
27DAP/17DAP	1.0532	0.92
39DAP/27DAP	0.94136	0.641
41DAP/39DAP	1.22168	0.298
42DAP/41DAP	1.10405	0.938
43DAP/42DAP	0.90036	0.77
47DAP/43DAP	0.90689	0.595
52DAP/47DAP	1.41757	0.466
57DAP/52DAP	1.15028	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29142	0.007
17DAP/reference	1.02558	0.528
27DAP/reference	1.08873	0.394
39DAP/reference	0.96743	0.487
41DAP/reference	1.00149	1
42DAP/reference	0.91586	0.043
43DAP/reference	0.99516	0.84
47DAP/reference	0.90174	0.05
52DAP/reference	1.01327	1
57DAP/reference	0.95698	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84787	0.078
27DAP/17DAP	0.99098	0.943
39DAP/27DAP	1.1305	0.429
41DAP/39DAP	1.02826	1
42DAP/41DAP	0.92761	0.402
43DAP/42DAP	0.97445	0.751
47DAP/43DAP	0.97722	0.909
52DAP/47DAP	0.97189	0.9
57DAP/52DAP	1.12949	0.8
57DAP/7DAP	1.96096

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97089	0.55
17DAP/reference	0.79615	0.124
27DAP/reference	0.81575	0.031
39DAP/reference	0.92689	0.073
41DAP/reference	0.8817	0.127
42DAP/reference	0.79472	0.032
43DAP/reference	0.75219	0.038
47DAP/reference	0.91922	0.383
52DAP/reference	0.84191	0.066
57DAP/reference	0.87815	0.114

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17511	0.041
17DAP/reference	1.10026	0.271
27DAP/reference	0.92202	0.16
39DAP/reference	1.11396	0.529
41DAP/reference	0.89686	0.063
42DAP/reference	0.85538	0.073
43DAP/reference	0.90208	0.292
47DAP/reference	0.94877	0.184
52DAP/reference	0.96809	0.537
57DAP/reference	0.86983	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85738	0.077
17DAP/reference	0.94208	0.444
27DAP/reference	0.71303	0.049
39DAP/reference	0.82143	0.025
41DAP/reference	0.82237	0.096
42DAP/reference	0.82207	0.134
43DAP/reference	0.77449	0.019
47DAP/reference	0.86438	0.054
52DAP/reference	0.75816	0.128
57DAP/reference	0.87372	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09357	0.966
26DAP/20DAP	1.04944	1
34DAP/26DAP	0.99946	1
51DAP/34DAP	1.01584	0.949
52DAP/51DAP	0.95035	1
53DAP/52DAP	0.95816	0.772
55DAP/53DAP	1.06739	0.876
57DAP/55DAP	0.85126	0.532
62DAP/57DAP	0.99247
68DAP/62DAP	2.18868	0.664
68DAP/14DAP	1.10752	0.403

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7862	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.9862	0.058
Mature Green Tomato/Ripe Tomato	2.80747	0.017
Immature Eggplant/Mature Eggplant	0.70395	0.092
Ripe Pepper/Ripe Tomato	2.34598	1
Mature Eggplant/Ripe Tomato	1.9202	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93982
12-2/M82	N/A	N/A
12-4/M82	0.99115	1
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	1.198
5-3/M82	1.29195
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.92654
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.24078	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09193	1
IL12-4/WTpooled	0.94315	0.71
IL1-4/WTpooled	0.98477
WT/WTpooled	0.98058	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	0.93621	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10187	0.921
DC3000/delta hrp 6h	1.0353	1
DC3000/delta hrp 12h	0.91244	1
DC3000/delta hrp 24h	0.76907	0.083

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34762	0.229
DC3000 delta B/DC3000 delta AB	0.94848	0.71

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04569	1
Exp 36h	1.02437	1
Exp 60h	0.83244	0.29

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	0.99033	1
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)	0.92337	0.314
transgenic ySAMdc/azygous control (breaker)	1.06131	1
transgenic ySAMdc/azygous control (red)	0.92649	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00494	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87184	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96802	1
Manapal/WT (break)	0.94355	1
Manapal/WT (red)	1.09736	0.137