Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.18.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62807	0.02
27DAP/17DAP	1.24021	0.793
39DAP/27DAP	1.29036	0.638
41DAP/39DAP	0.71442	0.07
42DAP/41DAP	0.61563	0.397
43DAP/42DAP	0.98853	0.931
47DAP/43DAP	0.92332	0.701
52DAP/47DAP	1.59472	0.243
57DAP/52DAP	0.99692	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84023	0.217
17DAP/reference	0.98371	0.701
27DAP/reference	0.96984	0.623
39DAP/reference	0.83732	0.046
41DAP/reference	0.93443	0.434
42DAP/reference	0.97628	0.295
43DAP/reference	0.83969	0.123
47DAP/reference	1.01611	0.674
52DAP/reference	0.98599	0.58
57DAP/reference	0.9591	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30479	0.492
27DAP/17DAP	0.8155	0.312
39DAP/27DAP	0.90936	0.462
41DAP/39DAP	1.49769	0.015
42DAP/41DAP	0.77416	0.089
43DAP/42DAP	0.72858	0.038
47DAP/43DAP	1.18015	0.618
52DAP/47DAP	1.11084	0.766
57DAP/52DAP	1.14327	0.718
57DAP/7DAP	1.18069	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45129	0.066
17DAP/reference	1.79797	0.006
27DAP/reference	1.68544	0.007
39DAP/reference	2.0286	0.006
41DAP/reference	1.93784	0.013
42DAP/reference	2.06467	0.006
43DAP/reference	1.77319	0.009
47DAP/reference	1.63078	0.026
52DAP/reference	1.95801	0.007
57DAP/reference	1.61579	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87616	0.204
17DAP/reference	1.09277	0.303
27DAP/reference	0.92409	0.282
39DAP/reference	1.06458	0.588
41DAP/reference	0.96527	0.34
42DAP/reference	1.10264	0.176
43DAP/reference	0.88196	0.243
47DAP/reference	0.98862	0.59
52DAP/reference	1.01307	1
57DAP/reference	1.02066	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38281	0.079
17DAP/reference	1.05497	0.934
27DAP/reference	1.85983	0.02
39DAP/reference	1.59628	0.027
41DAP/reference	1.49927	0.104
42DAP/reference	1.43194	0.124
43DAP/reference	1.30357	0.28
47DAP/reference	0.89745	0.049
52DAP/reference	1.8013	0.082
57DAP/reference	1.00752	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20512	0.966
26DAP/20DAP	1.3232	0.689
34DAP/26DAP	1.58586	1
51DAP/34DAP	1.19736	0.814
52DAP/51DAP	1.04497	1
53DAP/52DAP	0.96631	0.938
55DAP/53DAP	1.02711	0.876
57DAP/55DAP	1.01434	0.961
62DAP/57DAP	1.40923	0.569
68DAP/62DAP	1.43098	0.265
68DAP/14DAP	0.85087	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.57154	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.25703	0.067
Mature Green Tomato/Ripe Tomato	1.37585	0.017
Immature Eggplant/Mature Eggplant	3.01478	0.053
Ripe Pepper/Ripe Tomato	2.26078	1
Mature Eggplant/Ripe Tomato	1.37597	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84947	0.907
1-1-2/M82	0.94204	1
12-2/M82	1.72747	0.281
12-4/M82	0.80401
1-3/M82	1.38423
2-1-1/M82	0.78416	0.92
2-1/M82	N/A	N/A
2-6/M82	0.98945
3-2/M82	3.48883	0.549
4-1-1/M82	0.95833
4-1/M82	N/A	N/A
4-3-2/M82	2.07582
4-3/M82	0.88375	1
5-3/M82	1.93391	1
6-2/M82	3.04962
6-3/M82	0.68402
7-1/M82	1.08951
7-2/M82	1.05697	0.282
9-3-2/M82	N/A	N/A

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	1.45013
IL12-4/WTpooled	1.05721	1
IL1-4/WTpooled	0.88045	0.699
WT/WTpooled	1.02465	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	0.98072	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05438	0.921
DC3000/delta hrp 6h	1.11105	1
DC3000/delta hrp 12h	0.91036	1
DC3000/delta hrp 24h	2.75493	0.033

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.55384	0.042
DC3000 delta B/DC3000 delta AB	1.28086	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.5181	1
Exp 36h	1.14384	1
Exp 60h	1.13112	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06142	1
Var 0h	1.11752	1
Var 12h I row2-row1	1.15382	0.58
Var 12h NI row2-row1	1.14848	0.649
Var 36h I row2-row1	1.07318	1
Var 36h NI row2-row1	0.99725	0.852
Var 60h I row2-row1	0.6436	0.285
Var 60h NI row2-row1	0.79784	0.301
Time course 0hI-0hNI	1.12246	0.451
Time course 12hI-12hNI	0.87466	0.357
Time course 36hI-36hNI	1.15825	0.19
Time course 60hI-60hNI	2.36252	0.008

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)	0.87053	0.391
transgenic ySAMdc/azygous control (breaker)	0.76208	0.173
transgenic ySAMdc/azygous control (red)	1.03631	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00367	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83203	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83014	1
Manapal/WT (break)	0.88424	1
Manapal/WT (red)	0.36775	0.315