Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9673	0.752
27DAP/17DAP	0.92008	0.843
39DAP/27DAP	1.30691	0.395
41DAP/39DAP	0.90206	0.6
42DAP/41DAP	1.09681	0.978
43DAP/42DAP	1.07739	0.937
47DAP/43DAP	0.91501	0.699
52DAP/47DAP	0.96733	0.856
57DAP/52DAP	1.24379	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3133	0.062
17DAP/reference	1.05697	0.813
27DAP/reference	0.98338	0.683
39DAP/reference	1.02362	1
41DAP/reference	0.9948	0.814
42DAP/reference	1.2046	0.001
43DAP/reference	1.00969	1
47DAP/reference	1.20798	0.012
52DAP/reference	1.06129	0.524
57DAP/reference	1.20357	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93398	0.542
27DAP/17DAP	1.33407	0.161
39DAP/27DAP	0.91267	0.607
41DAP/39DAP	1.26951	0.986
42DAP/41DAP	1.24364	0.663
43DAP/42DAP	0.98161	0.854
47DAP/43DAP	0.9094	0.457
52DAP/47DAP	1.20312	0.543
57DAP/52DAP	1.2232	0.388
57DAP/7DAP	1.37045	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.68733	0.024
17DAP/reference	2.12183	0.006
27DAP/reference	2.09884	0.006
39DAP/reference	2.46282	0.005
41DAP/reference	2.40067	0.008
42DAP/reference	2.5928	0.006
43DAP/reference	2.57842	0.008
47DAP/reference	1.96655	0.015
52DAP/reference	2.26038	0.008
57DAP/reference	1.85595	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99453	0.756
17DAP/reference	0.98742	0.499
27DAP/reference	1.17686	0.192
39DAP/reference	1.30377	0.034
41DAP/reference	1.34037	0.035
42DAP/reference	1.54651	0.008
43DAP/reference	0.70824	0.033
47DAP/reference	1.19077	0.028
52DAP/reference	1.01546	1
57DAP/reference	0.65535	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.22282	0.016
17DAP/reference	1.1816	0.376
27DAP/reference	2.08217	0.015
39DAP/reference	1.90945	0.007
41DAP/reference	1.58007	0.01
42DAP/reference	2.25041	0.007
43DAP/reference	1.97651	0.007
47DAP/reference	1.01231	1
52DAP/reference	1.98462	0.033
57DAP/reference	1.87991	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98846	1
26DAP/20DAP	1.55208	0.707
34DAP/26DAP	1.393	1
51DAP/34DAP	1.55909	0.637
52DAP/51DAP	1.44234	0.048
53DAP/52DAP	0.84409	0.094
55DAP/53DAP	1.16551	0.29
57DAP/55DAP	0.90677	0.577
62DAP/57DAP	2.428	0.069
68DAP/62DAP	0.84842	0.7
68DAP/14DAP	2.49289	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.90604	0.039

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54003	0.107
Mature Green Tomato/Ripe Tomato	1.33367	0.038
Immature Eggplant/Mature Eggplant	1.32836	0.053
Ripe Pepper/Ripe Tomato	0.76392	0.224
Mature Eggplant/Ripe Tomato	1.04971	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81999	0.907
1-1-2/M82	1.10223	1
12-2/M82	1.01228	1
12-4/M82	1.05135	1
1-3/M82	1.76436	0.255
2-1-1/M82	1.14211	0.439
2-1/M82	0.91891	1
2-6/M82	0.75255	1
3-2/M82	1.39845	0.549
4-1-1/M82	1.02107	1
4-1/M82	1.10758	1
4-3-2/M82	1.16132	0.508
4-3/M82	1.17329	1
5-3/M82	0.99019	1
6-2/M82	1.51856	1
6-3/M82	0.95914	1
7-1/M82	1.01656	1
7-2/M82	1.10342	1
9-3-2/M82	1.09871	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87265	0.321
IL2-6/WTpooled	0.96989	1
IL7-5/WTpooled	1.0719	1
IL7-3/WTpooled	0.92885	0.418
IL12-4/WTpooled	1.06637	0.785
IL1-4/WTpooled	1.07364	1
WT/WTpooled	1.06124	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	1.12872	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9712	1
DC3000/delta hrp 6h	1.00381	0.95
DC3000/delta hrp 12h	1.12283	1
DC3000/delta hrp 24h	1.38626	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16198	0.094
DC3000 delta B/DC3000 delta AB	1.0538	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92552	1
Exp 36h	1.6009	0.409
Exp 60h	1.6196	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.01765	1
transgenic ySAMdc/azygous control (breaker)	0.88941	0.251
transgenic ySAMdc/azygous control (red)	1.06034	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.40065	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8531	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03696	0.105
Manapal/WT (break)	1.05387	1
Manapal/WT (red)	0.98001	0.607