Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.15.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98207	0.839
27DAP/17DAP	0.92369	0.836
39DAP/27DAP	0.91661	0.549
41DAP/39DAP	1.01591	0.929
42DAP/41DAP	1.13134	0.894
43DAP/42DAP	1.05714	1
47DAP/43DAP	1.07922	0.95
52DAP/47DAP	0.89114	0.67
57DAP/52DAP	0.81086	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28758	0.02
17DAP/reference	1.28276	0.012
27DAP/reference	1.12921	0.135
39DAP/reference	1.1473	0.101
41DAP/reference	1.56822	0.014
42DAP/reference	1.24371	0.001
43DAP/reference	1.09486	0.617
47DAP/reference	1.1984	0.001
52DAP/reference	1.21167	0.056
57DAP/reference	1.05726	0.783

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91857	0.509
27DAP/17DAP	0.99693	0.943
39DAP/27DAP	1.17035	0.347
41DAP/39DAP	0.95692	0.893
42DAP/41DAP	1.12349	0.55
43DAP/42DAP	0.87435	0.079
47DAP/43DAP	1.00272	0.985
52DAP/47DAP	1.9042	0.06
57DAP/52DAP	2.20798	0.036
57DAP/7DAP	2.59489	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9586	0.445
17DAP/reference	0.86	0.028
27DAP/reference	0.84412	0.013
39DAP/reference	0.93912	0.083
41DAP/reference	0.94382	0.194
42DAP/reference	0.92876	0.144
43DAP/reference	0.86114	0.012
47DAP/reference	0.92593	0.504
52DAP/reference	0.78251	0.015
57DAP/reference	0.84381	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27455	0.05
17DAP/reference	1.53803	0.015
27DAP/reference	1.20395	0.128
39DAP/reference	1.2806	0.044
41DAP/reference	1.12889	0.309
42DAP/reference	1.27973	0.044
43DAP/reference	1.55367	0.049
47DAP/reference	1.33636	0.008
52DAP/reference	1.52622	0.006
57DAP/reference	1.68931	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07295	1
17DAP/reference	1.09304	0.511
27DAP/reference	0.99257	0.763
39DAP/reference	0.95358	0.393
41DAP/reference	0.97242	0.56
42DAP/reference	0.84698	0.134
43DAP/reference	1.05465	0.679
47DAP/reference	1.14665	0.339
52DAP/reference	0.74218	0.098
57DAP/reference	0.77102	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03495	1
26DAP/20DAP	2.15551	0.308
34DAP/26DAP	2.06165	1
51DAP/34DAP	1.32651	0.978
52DAP/51DAP	3.44387	0.096
53DAP/52DAP	0.75102	0.058
55DAP/53DAP	1.36752	0.046
57DAP/55DAP	0.63888	0.149
62DAP/57DAP	1.13455	0.833
68DAP/62DAP	1.33494	0.769
68DAP/14DAP	0.82431	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.34256	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.30875	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87237	0.605
1-1-2/M82	0.81003	0.958
12-2/M82	1.07681	1
12-4/M82	0.94924	1
1-3/M82	1.01307	0.248
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.09922	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.28716
4-1/M82	1.08304	0.853
4-3-2/M82	0.99044	1
4-3/M82	N/A	N/A
5-3/M82	1.0357	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	1.06074
9-3-2/M82	0.96855	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.11942
IL12-4/WTpooled	1.09827	1
IL1-4/WTpooled	1.46454	1
WT/WTpooled	0.88841	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	0.85715	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92673	1
DC3000/delta hrp 6h	0.82239	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.12517	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13362	0.073
DC3000 delta B/DC3000 delta AB	1.00302	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22109	1
Exp 36h	0.82406	0.699
Exp 60h	0.75715	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98083	1
Var 0h	0.90893	0.933
Var 12h I row2-row1	0.79543	0.338
Var 12h NI row2-row1	1.03928	1
Var 36h I row2-row1	1.00599	1
Var 36h NI row2-row1	1.1327	0.482
Var 60h I row2-row1	0.92062	0.293
Var 60h NI row2-row1	0.97237	1
Time course 0hI-0hNI	0.95299	0.711
Time course 12hI-12hNI	0.96093	0.65
Time course 36hI-36hNI	0.89322	0.119
Time course 60hI-60hNI	0.5445	0.006

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)	1.16879	0.699
transgenic ySAMdc/azygous control (breaker)	1.1323	0.248
transgenic ySAMdc/azygous control (red)	1.07326	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90306	0.065

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.72727	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.33524	0.307
Manapal/WT (break)	1.03039	1
Manapal/WT (red)	N/A	N/A