Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.14.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14185	0.912
27DAP/17DAP	1.07513	1
39DAP/27DAP	1.18028	0.87
41DAP/39DAP	0.92947	0.717
42DAP/41DAP	1.10203	0.999
43DAP/42DAP	1.01405	1
47DAP/43DAP	1.05232	0.95
52DAP/47DAP	1.1226	0.906
57DAP/52DAP	0.83937	0.833

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79652	0.041
17DAP/reference	0.73644	0.074
27DAP/reference	0.93606	0.417
39DAP/reference	0.81372	0.021
41DAP/reference	0.67774	0.01
42DAP/reference	0.81837	0.009
43DAP/reference	0.91931	0.093
47DAP/reference	0.94165	0.258
52DAP/reference	0.99797	0.73
57DAP/reference	1.22199	0.18

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83299	0.363
27DAP/17DAP	1.01189	1
39DAP/27DAP	1.18059	0.541
41DAP/39DAP	0.94167	0.885
42DAP/41DAP	1.18462	0.582
43DAP/42DAP	0.88499	0.256
47DAP/43DAP	1.13329	0.914
52DAP/47DAP	0.93019	0.677
57DAP/52DAP	1.06052	0.877
57DAP/7DAP	0.67584	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01892	1
17DAP/reference	1.10915	1
27DAP/reference	1.03723	0.974
39DAP/reference	1.18955	0.175
41DAP/reference	0.93781	0.326
42DAP/reference	1.04129	1
43DAP/reference	0.94493	0.351
47DAP/reference	0.82449	0.128
52DAP/reference	0.92897	0.398
57DAP/reference	1.2715	0.035

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72504	0.035
17DAP/reference	0.7023	0.017
27DAP/reference	0.88988	0.16
39DAP/reference	0.88868	0.064
41DAP/reference	0.93772	0.231
42DAP/reference	0.87247	0.073
43DAP/reference	0.72892	0.082
47DAP/reference	0.75091	0.007
52DAP/reference	0.83201	0.018
57DAP/reference	0.61346	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99548	0.699
17DAP/reference	0.8868	0.308
27DAP/reference	0.98083	0.566
39DAP/reference	1.17795	0.069
41DAP/reference	0.99711	0.754
42DAP/reference	1.14835	0.313
43DAP/reference	0.98059	0.59
47DAP/reference	0.91965	0.325
52DAP/reference	0.98991	0.573
57DAP/reference	1.16211	0.086

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12401	0.966
26DAP/20DAP	0.944	1
34DAP/26DAP	1.19818	0.819
51DAP/34DAP	1.10046	0.627
52DAP/51DAP	1.02135	0.925
53DAP/52DAP	1.0185	1
55DAP/53DAP	1.22882	0.247
57DAP/55DAP	0.78542	0.271
62DAP/57DAP	1.34343	0.098
68DAP/62DAP	3.13073	0.036
68DAP/14DAP	2.78471	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10381	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.89064
Mature Green Tomato/Ripe Tomato	1.44891	0.437
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.84931	0.293
Mature Eggplant/Ripe Tomato	2.03318	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04422	0.591
1-1-2/M82	1.01577	1
12-2/M82	N/A	N/A
12-4/M82	1.25623	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	1.08188	1
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	1.11001
5-3/M82	0.94213	0.447
6-2/M82	0.78221
6-3/M82	0.95662	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.96991

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8025	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.20077	0.362
IL12-4/WTpooled	0.94599	0.52
IL1-4/WTpooled	0.98451
WT/WTpooled	1.03786	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	0.94697	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91453	0.868
DC3000/delta hrp 6h	1.02243	0.95
DC3000/delta hrp 12h	0.9162	1
DC3000/delta hrp 24h	1.1339	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.42242

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	0.99681	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00558
Var 0h	0.94024	1
Var 12h I row2-row1	1.0391	0.736
Var 12h NI row2-row1	1.33953	0.649
Var 36h I row2-row1	0.96675	1
Var 36h NI row2-row1	0.73128	0.645
Var 60h I row2-row1	1.15718	0.562
Var 60h NI row2-row1	1.22326	0.904
Time course 0hI-0hNI	1.0789	0.764
Time course 12hI-12hNI	0.95473	0.546
Time course 36hI-36hNI	0.98055	0.559
Time course 60hI-60hNI	1.12429	0.115

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)	0.95642	0.338
transgenic ySAMdc/azygous control (breaker)	1.0651	1
transgenic ySAMdc/azygous control (red)	0.88772	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99516	0.757

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17274	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77464	1
Manapal/WT (break)	0.7385	0.333
Manapal/WT (red)	0.80074	0.187