Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92647	0.664
27DAP/17DAP	0.92638	0.945
39DAP/27DAP	1.68938	0.188
41DAP/39DAP	2.87224	0.084
42DAP/41DAP	7.88397	0.016
43DAP/42DAP	4.57104	0.541
47DAP/43DAP	1.5963	0.369
52DAP/47DAP	0.35851	0.033
57DAP/52DAP	2.17002	0.771

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68412	0.007
17DAP/reference	1.32491	0.108
27DAP/reference	1.4879	0.033
39DAP/reference	0.81054	0.106
41DAP/reference	0.73882	0.016
42DAP/reference	1.20914	0.004
43DAP/reference	0.73147	0.015
47DAP/reference	0.59489	0.001
52DAP/reference	0.5046	0.013
57DAP/reference	0.82196	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26394	0.708
27DAP/17DAP	0.97498	0.878
39DAP/27DAP	1.40033	0.27
41DAP/39DAP	0.60288	0.108
42DAP/41DAP	1.53375	0.032
43DAP/42DAP	2.07055	0.013
47DAP/43DAP	0.89248	0.457
52DAP/47DAP	2.59089	0.041
57DAP/52DAP	1.16403	0.891
57DAP/7DAP	2.53849	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.0908	0.024
17DAP/reference	1.25582	0.18
27DAP/reference	1.08687	0.301
39DAP/reference	0.86526	0.083
41DAP/reference	0.69289	0.017
42DAP/reference	0.8609	0.037
43DAP/reference	0.97604	0.48
47DAP/reference	0.66863	0.044
52DAP/reference	0.71643	0.02
57DAP/reference	0.82091	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48216	0.067
17DAP/reference	1.5948	0.008
27DAP/reference	1.23558	0.139
39DAP/reference	0.63674	0.011
41DAP/reference	0.7932	0.034
42DAP/reference	1.02453	0.843
43DAP/reference	0.64321	0.011
47DAP/reference	0.65159	0.014
52DAP/reference	0.54042	0.003
57DAP/reference	0.50984	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.86855	0.015
17DAP/reference	1.66739	0.092
27DAP/reference	1.74123	0.018
39DAP/reference	1.06189	0.578
41DAP/reference	0.91912	0.264
42DAP/reference	1.0877	0.848
43DAP/reference	1.07358	0.49
47DAP/reference	0.85197	0.069
52DAP/reference	1.11142	0.888
57DAP/reference	0.89766	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06402	0.966
26DAP/20DAP	1.02476	1
34DAP/26DAP	0.89318	0.596
51DAP/34DAP	0.95331	0.737
52DAP/51DAP	1.31219	0.13
53DAP/52DAP	0.86893	0.535
55DAP/53DAP	1.10665	0.927
57DAP/55DAP	0.9771	0.664
62DAP/57DAP	1.31257	0.081
68DAP/62DAP	0.90011	0.7
68DAP/14DAP	0.57074	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	13.7571	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.5335	0.058
Mature Green Tomato/Ripe Tomato	0.02886	0.014
Immature Eggplant/Mature Eggplant	0.24387	0.057
Ripe Pepper/Ripe Tomato	13.3361	0.258
Mature Eggplant/Ripe Tomato	40.4636	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.35503	1
12-2/M82	1.04363	1
12-4/M82	2.40823	1
1-3/M82	N/A	N/A
2-1-1/M82	0.38636
2-1/M82	0.36972
2-6/M82	1.96031	0.329
3-2/M82	0.91942	1
4-1-1/M82	N/A	N/A
4-1/M82	3.79919
4-3-2/M82	1.43307	0.241
4-3/M82	N/A	N/A
5-3/M82	0.7489	1
6-2/M82	1.9115
6-3/M82	N/A	N/A
7-1/M82	0.76734	0.803
7-2/M82	1.61566
9-3-2/M82	1.94164	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14053	0.365
IL2-6/WTpooled	1.0338	0.788
IL7-5/WTpooled	0.71976
IL7-3/WTpooled	1.11304	1
IL12-4/WTpooled	1.03302	0.891
IL1-4/WTpooled	1.09174	1
WT/WTpooled	0.93387	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	0.89206	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98716	1
DC3000/delta hrp 6h	0.95651	0.95
DC3000/delta hrp 12h	1.03954	1
DC3000/delta hrp 24h	0.44245	0.034

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	0.80699

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91103	1
Exp 36h	0.79166	0.539
Exp 60h	0.69772	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.6628	1
Var 0h	0.96966	1
Var 12h I row2-row1	0.85894	0.338
Var 12h NI row2-row1	1.10928	1
Var 36h I row2-row1	0.89436	1
Var 36h NI row2-row1	0.81445	0.645
Var 60h I row2-row1	1.02006	1
Var 60h NI row2-row1	0.6355	0.818
Time course 0hI-0hNI	1.02151	0.867
Time course 12hI-12hNI	0.92532	0.575
Time course 36hI-36hNI	0.99472	0.73
Time course 60hI-60hNI	0.58928	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)	0.95164	0.409
transgenic ySAMdc/azygous control (breaker)	0.85406	0.49
transgenic ySAMdc/azygous control (red)	5.29504	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8358	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.94484	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.60701	0.14
Manapal/WT (break)	2.95793	0.183
Manapal/WT (red)	1.91951	0.15