Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.20.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92894	0.617
27DAP/17DAP	1.38404	0.663
39DAP/27DAP	1.20221	0.765
41DAP/39DAP	0.9635	0.771
42DAP/41DAP	0.84488	1
43DAP/42DAP	0.9144	0.801
47DAP/43DAP	0.78791	0.366
52DAP/47DAP	1.08489	0.943
57DAP/52DAP	1.00063	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99218	0.679
17DAP/reference	1.15324	0.631
27DAP/reference	1.07425	0.831
39DAP/reference	1.00959	0.841
41DAP/reference	0.99867	1
42DAP/reference	1.03975	0.963
43DAP/reference	0.99764	0.805
47DAP/reference	0.80737
52DAP/reference	1.10325	0.576
57DAP/reference	1.11189	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09061	0.445
27DAP/17DAP	1.07594	0.893
39DAP/27DAP	1.108	0.659
41DAP/39DAP	1.27127	0.266
42DAP/41DAP	1.0976	0.478
43DAP/42DAP	1.0537	0.746
47DAP/43DAP	1.03115	0.957
52DAP/47DAP	0.97257	0.902
57DAP/52DAP	0.93149	0.641
57DAP/7DAP	1.51285	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82114	0.183
17DAP/reference	0.824	0.025
27DAP/reference	0.88322	0.058
39DAP/reference	0.7164	0.011
41DAP/reference	0.53666	0.011
42DAP/reference	0.64417	0.01
43DAP/reference	0.76382	0.017
47DAP/reference	0.75572	0.222
52DAP/reference	0.70672	0.013
57DAP/reference	0.71761	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67597	0.009
17DAP/reference	0.6132	0.003
27DAP/reference	0.66635	0.16
39DAP/reference	1.03154	0.722
41DAP/reference	0.74651	0.036
42DAP/reference	0.37397	0.02
43DAP/reference	1.35148	0.124
47DAP/reference	0.95021
52DAP/reference	0.88766	0.04
57DAP/reference	1.26489	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93619	0.391
17DAP/reference	0.87125	0.112
27DAP/reference	0.75893	0.051
39DAP/reference	0.93218	0.299
41DAP/reference	0.83554	0.077
42DAP/reference	0.91478	0.287
43DAP/reference	0.76395	0.092
47DAP/reference	0.9076	0.259
52DAP/reference	1.15315	0.946
57DAP/reference	0.70411	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99513	1
26DAP/20DAP	1.06845	0.798
34DAP/26DAP	0.91172	0.735
51DAP/34DAP	0.95181	0.714
52DAP/51DAP	0.79143	1
53DAP/52DAP	1.31001	0.196
55DAP/53DAP	0.92576	0.648
57DAP/55DAP	1.20072	0.87
62DAP/57DAP	0.71562	0.01
68DAP/62DAP	1.32622	0.737
68DAP/14DAP	1.16252	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20002	0.184

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.56994
Mature Green Tomato/Ripe Tomato	1.10625	0.478
Immature Eggplant/Mature Eggplant	1.70645	0.05
Ripe Pepper/Ripe Tomato	0.984	1
Mature Eggplant/Ripe Tomato	1.11454	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98527	0.944
1-1-2/M82	1.07805
12-2/M82	N/A	N/A
12-4/M82	0.97493	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.9504
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.82696
5-3/M82	1.04648	1
6-2/M82	N/A	N/A
6-3/M82	0.97684	1
7-1/M82	1.13959
7-2/M82	1.04166
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82916	0.321
IL2-6/WTpooled	0.98901	1
IL7-5/WTpooled	1.16041	1
IL7-3/WTpooled	0.78081	0.294
IL12-4/WTpooled	1.39761	0.503
IL1-4/WTpooled	0.97268	0.834
WT/WTpooled	1.08931	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	0.90043	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11619	0.914
DC3000/delta hrp 6h	1.0332	1
DC3000/delta hrp 12h	1.14125	1
DC3000/delta hrp 24h	0.95637	0.861

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83212	1
Exp 36h	0.8856	0.749
Exp 60h	0.95843	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98461	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.96999	0.856
Var 12h NI row2-row1	1.16303	0.281
Var 36h I row2-row1	1.05	1
Var 36h NI row2-row1	1.00971	0.852
Var 60h I row2-row1	0.81849	0.832
Var 60h NI row2-row1	0.98019	1
Time course 0hI-0hNI	1.02345	1
Time course 12hI-12hNI	1.05313	0.663
Time course 36hI-36hNI	0.87323	0.121
Time course 60hI-60hNI	1.1111	0.096

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)	1.01839	0.921
transgenic ySAMdc/azygous control (breaker)	0.53177	0.125
transgenic ySAMdc/azygous control (red)	0.98304	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09349	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03125	0.307
Manapal/WT (break)	0.71441	0.299
Manapal/WT (red)	0.70588	0.181