Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02688	0.801
27DAP/17DAP	0.56644	0.075
39DAP/27DAP	0.63865	0.326
41DAP/39DAP	0.59454	0.047
42DAP/41DAP	0.94044	1
43DAP/42DAP	1.27316	0.682
47DAP/43DAP	0.39432	0.049
52DAP/47DAP	1.45872	0.608
57DAP/52DAP	0.94062	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80079	0.08
17DAP/reference	0.58966	0.01
27DAP/reference	0.61337	0.015
39DAP/reference	0.47188	0.012
41DAP/reference	0.48685	0.012
42DAP/reference	0.6571	0.002
43DAP/reference	0.58982	0.012
47DAP/reference	0.61451	0.002
52DAP/reference	0.62739	0.036
57DAP/reference	0.75826	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.93201	0.036
27DAP/17DAP	0.72896	0.218
39DAP/27DAP	0.41324	0.034
41DAP/39DAP	1.38279	0.163
42DAP/41DAP	0.82517	0.141
43DAP/42DAP	0.50768	0.022
47DAP/43DAP	0.92159	0.63
52DAP/47DAP	1.03344	0.965
57DAP/52DAP	1.24198	0.493
57DAP/7DAP	0.39877	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90318	0.086
17DAP/reference	1.00592	0.599
27DAP/reference	0.97643	0.494
39DAP/reference	1.01982	1
41DAP/reference	1.05358	1
42DAP/reference	1.15333	0.233
43DAP/reference	0.88758	0.175
47DAP/reference	0.73705	0.128
52DAP/reference	0.98925	0.523
57DAP/reference	0.97011	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67745	0.046
17DAP/reference	0.78214	0.023
27DAP/reference	0.96807	0.452
39DAP/reference	0.71737	0.108
41DAP/reference	0.9818	0.459
42DAP/reference	0.8244	0.042
43DAP/reference	0.59708	0.028
47DAP/reference	0.54238	0.007
52DAP/reference	0.5646	0.004
57DAP/reference	0.282	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02085	1
17DAP/reference	1.36092	0.217
27DAP/reference	0.94552	0.416
39DAP/reference	0.86057	0.092
41DAP/reference	1.00278	0.754
42DAP/reference	1.14884	0.635
43DAP/reference	1.08177	0.935
47DAP/reference	0.72384	0.097
52DAP/reference	0.61878	0.15
57DAP/reference	1.66534	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.853	1
26DAP/20DAP	1.15576	0.567
34DAP/26DAP	0.79544	0.142
51DAP/34DAP	0.42389	0.049
52DAP/51DAP	1.09764	0.413
53DAP/52DAP	0.5576	0.049
55DAP/53DAP	0.71652	0.098
57DAP/55DAP	0.87762	0.486
62DAP/57DAP	1.44636	0.024
68DAP/62DAP	1.18053	0.89
68DAP/14DAP	1.11992	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.38839	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.30792	0.058
Mature Green Tomato/Ripe Tomato	12.376	0.015
Immature Eggplant/Mature Eggplant	0.52167	0.057
Ripe Pepper/Ripe Tomato	2.52673	0.236
Mature Eggplant/Ripe Tomato	8.69781

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.54711	0.243
IL2-6/WTpooled	0.84771	0.473
IL7-5/WTpooled	0.60953	1
IL7-3/WTpooled	0.81294	0.298
IL12-4/WTpooled	0.71981	0.581
IL1-4/WTpooled	0.77487	0.457
WT/WTpooled	1.05578	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	1.00386	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91127	1
DC3000/delta hrp 6h	1.03185	1
DC3000/delta hrp 12h	1.20504	1
DC3000/delta hrp 24h	0.71618	0.092

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.89287	0.436
DC3000 delta B/DC3000 delta AB	0.51715	0.03

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02771	1
Exp 36h	0.81133	0.539
Exp 60h	0.90558	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9916	1
Var 0h	0.84006	1
Var 12h I row2-row1	1.04208	0.692
Var 12h NI row2-row1	1.03805	0.649
Var 36h I row2-row1	0.97383	1
Var 36h NI row2-row1	0.93607	0.61
Var 60h I row2-row1	1.19659	0.502
Var 60h NI row2-row1	0.95308	0.63
Time course 0hI-0hNI	0.98976	0.999
Time course 12hI-12hNI	1.04587	0.621
Time course 36hI-36hNI	1.03347	0.651
Time course 60hI-60hNI	0.74951	0.047

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)	1.13339	0.612
transgenic ySAMdc/azygous control (breaker)	1.49853	0.166
transgenic ySAMdc/azygous control (red)	1.09755	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.5788	0.12

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.7085	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	12.4572	0.083
Manapal/WT (break)	5.11878	0.123
Manapal/WT (red)	1.62798	0.413