Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.15.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97493	0.752
27DAP/17DAP	1.13802	0.833
39DAP/27DAP	0.99384	0.82
41DAP/39DAP	1.1925	0.423
42DAP/41DAP	0.86836	1
43DAP/42DAP	0.95589	0.867
47DAP/43DAP	1.26157	0.187
52DAP/47DAP	1.18642	0.757
57DAP/52DAP	0.91481	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74158	0.07
17DAP/reference	0.58087	0.012
27DAP/reference	0.89621	0.314
39DAP/reference	0.78117	0.012
41DAP/reference	0.57908	0.016
42DAP/reference	0.96797	0.348
43DAP/reference	0.93007	0.36
47DAP/reference	1.03201	0.989
52DAP/reference	1.49626	0.008
57DAP/reference	1.32163	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.50449	0.124
27DAP/17DAP	0.9992	0.943
39DAP/27DAP	0.70349	0.06
41DAP/39DAP	1.10163	0.986
42DAP/41DAP	1.57541	0.011
43DAP/42DAP	0.83534	0.172
47DAP/43DAP	0.8514	0.365
52DAP/47DAP	1.90781	0.422
57DAP/52DAP	2.2732	0.053
57DAP/7DAP	2.62065	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03268	0.843
17DAP/reference	0.99855	0.693
27DAP/reference	0.98801	0.571
39DAP/reference	1.05895	0.779
41DAP/reference	1.01137	1
42DAP/reference	0.98652	0.554
43DAP/reference	0.94059	0.321
47DAP/reference	1.12037	0.377
52DAP/reference	1.01687	1
57DAP/reference	1.02557	0.775

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70073	0.049
17DAP/reference	0.5871	0.004
27DAP/reference	0.89953	0.24
39DAP/reference	1.14056	0.556
41DAP/reference	1.02564	1
42DAP/reference	1.10544	0.302
43DAP/reference	0.73161	0.068
47DAP/reference	0.83553	0.039
52DAP/reference	0.99746	0.713
57DAP/reference	0.59303	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04771	1
17DAP/reference	0.81878	0.308
27DAP/reference	0.90705	0.257
39DAP/reference	0.9405	0.179
41DAP/reference	0.9477	0.371
42DAP/reference	1.1992	0.142
43DAP/reference	1.23091	0.19
47DAP/reference	1.07631	0.877
52DAP/reference	0.89556	0.368
57DAP/reference	1.72566	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0011	1
26DAP/20DAP	5.72265	0.642
34DAP/26DAP	6.69503	1
51DAP/34DAP	2.88123	0.597
52DAP/51DAP	6.90551	0.034
53DAP/52DAP	0.59026	0.059
55DAP/53DAP	2.09212
57DAP/55DAP	0.40204	0.035
62DAP/57DAP	1.89387	0.133
68DAP/62DAP	4.80677	0.011
68DAP/14DAP	7.31178	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.1346	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23201	0.089
Mature Green Tomato/Ripe Tomato	0.76234	0.132
Immature Eggplant/Mature Eggplant	1.56256	0.05
Ripe Pepper/Ripe Tomato	0.29343	0.224
Mature Eggplant/Ripe Tomato	0.34286	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.88135	0.742
1-1-2/M82	1.17093	1
12-2/M82	1.06172	1
12-4/M82	0.79631	0.33
1-3/M82	1.13208	1
2-1-1/M82	0.73273	0.465
2-1/M82	0.73385	0.74
2-6/M82	1.19699	0.385
3-2/M82	1.58797
4-1-1/M82	0.80616	1
4-1/M82	0.83045	1
4-3-2/M82	0.79864	0.458
4-3/M82	1.36727	1
5-3/M82	1.17153	1
6-2/M82	0.63415	1
6-3/M82	0.95863	1
7-1/M82	0.71122
7-2/M82	1.29498	0.385
9-3-2/M82	0.73155

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.05406	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94972	1
DC3000/delta hrp 6h	1.09057	1
DC3000/delta hrp 12h	1.23487	1
DC3000/delta hrp 24h	1.27505	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.70498	0.042
DC3000 delta B/DC3000 delta AB	1.60952	0.176

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00004	1
Exp 36h	1.07263	1
Exp 60h	1.10305	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99426	1
Var 0h	0.43885	1
Var 12h I row2-row1	0.75545	0.514
Var 12h NI row2-row1	1.1698	0.649
Var 36h I row2-row1	1.24271	1
Var 36h NI row2-row1	1.88246	0.482
Var 60h I row2-row1	0.68439	0.285
Var 60h NI row2-row1	1.05188	1
Time course 0hI-0hNI	0.90641	0.482
Time course 12hI-12hNI	1.10983	1
Time course 36hI-36hNI	0.98996	0.373
Time course 60hI-60hNI	0.90279	0.319

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)	1.03607	0.699
transgenic ySAMdc/azygous control (breaker)	1.08233	0.248
transgenic ySAMdc/azygous control (red)	1.06681	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03808	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90077	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64445	0.172
Manapal/WT (break)	0.76344	0.299
Manapal/WT (red)	1.54347	0.413