Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.19.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99258	0.76
27DAP/17DAP	0.9124	0.922
39DAP/27DAP	0.62469	0.263
41DAP/39DAP	1.05257	0.852
42DAP/41DAP	0.82904	1
43DAP/42DAP	1.50171	0.918
47DAP/43DAP	1.29234	0.909
52DAP/47DAP	1.17057	0.837
57DAP/52DAP	1.01771	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00539	1
17DAP/reference	1.02293	0.631
27DAP/reference	1.01389	0.831
39DAP/reference	1.03127	0.534
41DAP/reference	0.98858	0.814
42DAP/reference	0.98531	0.425
43DAP/reference	0.99677	0.904
47DAP/reference	0.97682	0.445
52DAP/reference	0.88365	0.121
57DAP/reference	0.95005	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12386	0.196
27DAP/17DAP	0.96858	0.887
39DAP/27DAP	0.94738	0.66
41DAP/39DAP	0.93987	0.793
42DAP/41DAP	1.04911	0.947
43DAP/42DAP	1.04078	0.699
47DAP/43DAP	1.22223	0.036
52DAP/47DAP	0.98304	0.917
57DAP/52DAP	1.24185	0.382
57DAP/7DAP	1.18172	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10103	0.555
17DAP/reference	1.10722	0.102
27DAP/reference	1.0592	0.301
39DAP/reference	1.2097	0.025
41DAP/reference	1.06412	0.363
42DAP/reference	1.23302	0.007
43DAP/reference	1.45861	0.006
47DAP/reference	1.05314	0.996
52DAP/reference	1.45743	0.009
57DAP/reference	1.48171	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03186	0.732
17DAP/reference	0.92737	0.116
27DAP/reference	0.91194	0.195
39DAP/reference	0.90637	0.147
41DAP/reference	0.8806	0.068
42DAP/reference	1.00106	0.723
43DAP/reference	0.93429	0.285
47DAP/reference	0.97929	0.446
52DAP/reference	0.99848	0.761
57DAP/reference	1.07426	0.161

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03542	0.827
17DAP/reference	0.94058	0.342
27DAP/reference	0.86377	0.062
39DAP/reference	0.89496	0.023
41DAP/reference	0.95021	0.459
42DAP/reference	0.95337	0.361
43DAP/reference	0.98046	0.523
47DAP/reference	0.95785	0.409
52DAP/reference	0.95283	0.551
57DAP/reference	0.84753	0.082

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97239	1
26DAP/20DAP	1.29889	0.302
34DAP/26DAP	0.87546	0.653
51DAP/34DAP	0.91123	0.624
52DAP/51DAP	1.2362	0.271
53DAP/52DAP	0.80146	0.527
55DAP/53DAP	1.01106	0.864
57DAP/55DAP	0.979	0.888
62DAP/57DAP	1.10633	0.515
68DAP/62DAP	1.28088	0.507
68DAP/14DAP	0.9422	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78799	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87039	0.364
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.15639	0.157
Ripe Pepper/Ripe Tomato	0.63042	0.224
Mature Eggplant/Ripe Tomato	0.57484	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02478	1
1-1-2/M82	0.78201	0.958
12-2/M82	0.96492	0.955
12-4/M82	0.9587	1
1-3/M82	0.90744	0.501
2-1-1/M82	0.90769	0.465
2-1/M82	1.03448	1
2-6/M82	0.98058	1
3-2/M82	1.05553
4-1-1/M82	0.99412	1
4-1/M82	0.93402
4-3-2/M82	1.00058
4-3/M82	0.83784	0.72
5-3/M82	0.99538	1
6-2/M82	1.03144	1
6-3/M82	1.05556	1
7-1/M82	0.99024	0.803
7-2/M82	0.97139	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13139	0.277
IL2-6/WTpooled	0.82513	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.28096	1
IL12-4/WTpooled	1.07027	0.839
IL1-4/WTpooled	1.05309	0.378
WT/WTpooled	0.99544	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	1.06548	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88886	1
DC3000/delta hrp 6h	1.20057	1
DC3000/delta hrp 12h	0.96064	1
DC3000/delta hrp 24h	1.2008	0.271

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	0.68171

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96593	1
Exp 36h	1.2461	1
Exp 60h	1.06111	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03313	1
Var 0h	0.69564	1
Var 12h I row2-row1	2.08641	0.348
Var 12h NI row2-row1	0.50431	0.713
Var 36h I row2-row1	1.08093	1
Var 36h NI row2-row1	0.90686	0.743
Var 60h I row2-row1	0.8697	0.832
Var 60h NI row2-row1	1.56923	0.904
Time course 0hI-0hNI	0.93139	0.675
Time course 12hI-12hNI	1.15602	0.58
Time course 36hI-36hNI	1.63983	0.035
Time course 60hI-60hNI	1.72762	0.01

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)	1.17753	0.571
transgenic ySAMdc/azygous control (breaker)	0.62624	0.118
transgenic ySAMdc/azygous control (red)	1.07408	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96977	0.196

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08223	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7958	0.172
Manapal/WT (break)	0.88003	1
Manapal/WT (red)	0.61072	0.181