Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.2.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08499	0.786
27DAP/17DAP	0.77457	0.206
39DAP/27DAP	0.95596	0.663
41DAP/39DAP	0.9194	0.641
42DAP/41DAP	1.05188	0.929
43DAP/42DAP	0.99455	0.937
47DAP/43DAP	0.82855	0.467
52DAP/47DAP	1.03772	0.971
57DAP/52DAP	1.28633	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03011	0.928
17DAP/reference	0.99327	0.819
27DAP/reference	1.01749	0.709
39DAP/reference	0.97203	0.6
41DAP/reference	0.9478	0.201
42DAP/reference	1.10967	0.191
43DAP/reference	0.95626	0.36
47DAP/reference	1.05302	0.114
52DAP/reference	1.18992	0.229
57DAP/reference	1.26558	0.132

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10657	0.379
27DAP/17DAP	1.06809	0.842
39DAP/27DAP	0.78618	0.069
41DAP/39DAP	0.99	1
42DAP/41DAP	0.97791	0.768
43DAP/42DAP	1.0436	0.413
47DAP/43DAP	0.90377	0.175
52DAP/47DAP	1.02808	0.892
57DAP/52DAP	0.96087	0.709
57DAP/7DAP	0.82741	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9305	0.224
17DAP/reference	0.90615	0.012
27DAP/reference	0.85867	0.01
39DAP/reference	0.85459	0.013
41DAP/reference	0.89535	0.076
42DAP/reference	0.82326	0.011
43DAP/reference	0.83472	0.02
47DAP/reference	0.92307	0.168
52DAP/reference	0.83427	0.012
57DAP/reference	0.83278	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09102	0.279
17DAP/reference	1.0451	0.338
27DAP/reference	1.14416	0.062
39DAP/reference	1.16762	0.213
41DAP/reference	1.20442	0.081
42DAP/reference	1.062	0.519
43DAP/reference	1.01759	0.91
47DAP/reference	0.95588	0.221
52DAP/reference	1.0846	0.061
57DAP/reference	1.05369	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93337	0.268
17DAP/reference	0.99	0.763
27DAP/reference	0.87477	0.067
39DAP/reference	0.88162	0.076
41DAP/reference	0.88834	0.055
42DAP/reference	0.94261	0.552
43DAP/reference	0.98323	0.614
47DAP/reference	1.00591	1
52DAP/reference	0.93022	0.464
57DAP/reference	1.40744	0.068

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98951	1
26DAP/20DAP	1.43801	0.319
34DAP/26DAP	1.31972	1
51DAP/34DAP	1.20025	0.387
52DAP/51DAP	1.37219	0.083
53DAP/52DAP	1.02451	1
55DAP/53DAP	1.19319	0.576
57DAP/55DAP	0.80935	0.178
62DAP/57DAP	1.02235	0.935
68DAP/62DAP	0.92814	0.769
68DAP/14DAP	1.11359	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99647	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00853	1
Mature Green Tomato/Ripe Tomato	1.37894	0.036
Immature Eggplant/Mature Eggplant	0.9729	0.808
Ripe Pepper/Ripe Tomato	2.30737	0.258
Mature Eggplant/Ripe Tomato	1.43039	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0107	1
1-1-2/M82	0.9528	1
12-2/M82	0.92536	0.955
12-4/M82	0.98507	1
1-3/M82	0.98771	1
2-1-1/M82	0.97738	0.92
2-1/M82	1.15863	1
2-6/M82	0.96444	1
3-2/M82	1.00116	1
4-1-1/M82	1.03605	1
4-1/M82	0.92567
4-3-2/M82	0.9503
4-3/M82	0.93315	0.72
5-3/M82	1.03806	0.572
6-2/M82	1.01778	1
6-3/M82	0.96006	1
7-1/M82	0.99658	1
7-2/M82	0.88544	0.796
9-3-2/M82	0.99337

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.24111	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.99097
IL1-4/WTpooled	1.68973
WT/WTpooled	0.8407	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	0.87231	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0115	1
DC3000/delta hrp 6h	0.97361	0.95
DC3000/delta hrp 12h	0.99271	1
DC3000/delta hrp 24h	1.00766	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87429	0.088
DC3000 delta B/DC3000 delta AB	0.83588	0.152

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.42765	1
Exp 36h	0.98883	1
Exp 60h	0.97819	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98095	1
Var 0h	0.94115	1
Var 12h I row2-row1	1.05977	0.473
Var 12h NI row2-row1	1.07761	1
Var 36h I row2-row1	0.94166	0.805
Var 36h NI row2-row1	1.20318	1
Var 60h I row2-row1	0.90379	0.374
Var 60h NI row2-row1	0.9841	1
Time course 0hI-0hNI	0.94808	0.615
Time course 12hI-12hNI	1.00338	1
Time course 36hI-36hNI	0.92365	0.125
Time course 60hI-60hNI	1.13098	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)	0.96703	0.306
transgenic ySAMdc/azygous control (breaker)	0.77478	0.251
transgenic ySAMdc/azygous control (red)	0.98932	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99576	0.737

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99862	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01943	1
Manapal/WT (break)	0.99861	1
Manapal/WT (red)	0.7568	0.181