Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.8.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14217	0.561
27DAP/17DAP	1.51389	0.552
39DAP/27DAP	0.81794	0.474
41DAP/39DAP	1.2295	0.447
42DAP/41DAP	1.27957	0.882
43DAP/42DAP	1.14369	0.894
47DAP/43DAP	1.25762	0.555
52DAP/47DAP	0.70165	0.246
57DAP/52DAP	1.13452	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9329	0.3
17DAP/reference	0.97663	0.597
27DAP/reference	0.90292	0.034
39DAP/reference	0.96981	0.704
41DAP/reference	0.94383	0.341
42DAP/reference	0.94589	0.069
43DAP/reference	1.05988	0.287
47DAP/reference	0.97534	0.3
52DAP/reference	0.93609	0.25
57DAP/reference	0.90125	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21528	1
27DAP/17DAP	0.97222	0.614
39DAP/27DAP	1.40947	0.659
41DAP/39DAP	1.25925	0.817
42DAP/41DAP	1.52428	0.378
43DAP/42DAP	1.75597	0.513
47DAP/43DAP	0.92659	0.722
52DAP/47DAP	0.74824	0.66
57DAP/52DAP	1.09241	0.877
57DAP/7DAP	4.58557	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86269	0.168
17DAP/reference	0.80489	0.012
27DAP/reference	0.70704	0.01
39DAP/reference	0.81209	0.014
41DAP/reference	0.7874	0.016
42DAP/reference	0.73122	0.026
43DAP/reference	0.77433	0.025
47DAP/reference	0.80713	0.057
52DAP/reference	0.80811	0.031
57DAP/reference	0.86979	0.101

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03835	0.449
17DAP/reference	0.97854	0.561
27DAP/reference	0.98228	0.537
39DAP/reference	1.03573	0.746
41DAP/reference	0.91616	0.115
42DAP/reference	0.92959	0.039
43DAP/reference	0.94209	0.378
47DAP/reference	0.94648	0.221
52DAP/reference	0.92311	0.037
57DAP/reference	0.93497	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96049	0.489
17DAP/reference	0.9245	0.407
27DAP/reference	0.72894	0.027
39DAP/reference	0.71706	0.01
41DAP/reference	0.98646	0.618
42DAP/reference	0.83928	0.071
43DAP/reference	1.13631	0.296
47DAP/reference	0.88776	0.052
52DAP/reference	0.87344	0.289
57DAP/reference	0.95636	0.43

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97885	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.8717	0.712
51DAP/34DAP	0.98904	0.924
52DAP/51DAP	1.7378	0.404
53DAP/52DAP	1.04855	1
55DAP/53DAP	1.64147	0.608
57DAP/55DAP	1.12753	0.881
62DAP/57DAP	1.03641	0.723
68DAP/62DAP	1.06405	1
68DAP/14DAP	1.15424	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69699	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.46231	0.059
Mature Green Tomato/Ripe Tomato	0.66284	0.031
Immature Eggplant/Mature Eggplant	1.38613	0.052
Ripe Pepper/Ripe Tomato	0.51124	1
Mature Eggplant/Ripe Tomato	0.59574	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9467
1-1-2/M82	0.96645	1
12-2/M82	1.09387	0.61
12-4/M82	0.95226	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.26143
3-2/M82	0.96289
4-1-1/M82	0.82724
4-1/M82	0.6939	0.998
4-3-2/M82	0.97634	1
4-3/M82	0.8334	0.72
5-3/M82	0.96863	1
6-2/M82	1.2406
6-3/M82	1.38785
7-1/M82	1.18051
7-2/M82	1.13719
9-3-2/M82	0.84671	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86083	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.15969	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.26907
IL1-4/WTpooled	0.87878	1
WT/WTpooled	1.18244

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95132	1
DC3000/delta hrp 6h	1.05064	1
DC3000/delta hrp 12h	1.07576	1
DC3000/delta hrp 24h	1.12584	0.516

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	5.19357

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97433	1
Exp 36h	0.9232	0.82
Exp 60h	0.92525	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02749	1
Var 0h	0.83188	0.237
Var 12h I row2-row1	0.85311	0.705
Var 12h NI row2-row1	0.88478	0.82
Var 36h I row2-row1	1.05559
Var 36h NI row2-row1	1.12102	1
Var 60h I row2-row1	1.02309	1
Var 60h NI row2-row1	1.14242	1
Time course 0hI-0hNI	0.92761	0.799
Time course 12hI-12hNI	1.09179	0.836
Time course 36hI-36hNI	1.47039	0.012
Time course 60hI-60hNI	0.67	0.081

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)	0.77676	0.297
transgenic ySAMdc/azygous control (breaker)	1.20101	1
transgenic ySAMdc/azygous control (red)	1.01139	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02615	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04485	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08234	1
Manapal/WT (break)	0.99357	1
Manapal/WT (red)	0.85753	0.424