Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35522	0.365
27DAP/17DAP	0.58994	0.064
39DAP/27DAP	0.54871	0.253
41DAP/39DAP	0.60517	0.07
42DAP/41DAP	0.72088	0.774
43DAP/42DAP	1.2522	0.772
47DAP/43DAP	0.53695	0.065
52DAP/47DAP	0.94917	0.842
57DAP/52DAP	1.18716	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65674	0.026
17DAP/reference	0.85737	0.104
27DAP/reference	0.72399	0.02
39DAP/reference	0.73431	0.036
41DAP/reference	0.72576	0.031
42DAP/reference	0.58219	0.001
43DAP/reference	0.76391	0.045
47DAP/reference	0.55802	0.001
52DAP/reference	0.40624	0.013
57DAP/reference	0.64956	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.68064	0.036
27DAP/17DAP	0.73001	0.172
39DAP/27DAP	0.58436	0.045
41DAP/39DAP	1.1535	0.484
42DAP/41DAP	0.99854	0.902
43DAP/42DAP	0.82735	0.224
47DAP/43DAP	0.96959	0.855
52DAP/47DAP	0.98869	0.93
57DAP/52DAP	1.61345	0.483
57DAP/7DAP	0.59583	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08267	0.501
17DAP/reference	0.82464	0.064
27DAP/reference	0.53784	0.01
39DAP/reference	0.40459	0.011
41DAP/reference	0.35244	0.009
42DAP/reference	0.30208	0.01
43DAP/reference	0.27795	0.008
47DAP/reference	0.31049	0.026
52DAP/reference	0.3812	0.013
57DAP/reference	0.31823	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5657	0.005
17DAP/reference	0.61453	0.01
27DAP/reference	0.61679	0.014
39DAP/reference	0.46023	0.01
41DAP/reference	0.43655	0.006
42DAP/reference	0.57335	0.014
43DAP/reference	0.42399	0.005
47DAP/reference	0.63374	0.008
52DAP/reference	0.37204	0.003
57DAP/reference	0.35967	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.21904	0.015
17DAP/reference	1.9846	0.135
27DAP/reference	1.33307	0.078
39DAP/reference	1.10186	0.546
41DAP/reference	0.72755	0.019
42DAP/reference	0.47571	0.015
43DAP/reference	0.49892	0.019
47DAP/reference	0.47129	0.004
52DAP/reference	0.42765	0.05
57DAP/reference	0.68988	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91238	0.997
26DAP/20DAP	0.94655	1
34DAP/26DAP	0.86064	0.488
51DAP/34DAP	0.54751	0.057
52DAP/51DAP	0.96601	1
53DAP/52DAP	0.83997	0.157
55DAP/53DAP	1.03276	0.991
57DAP/55DAP	1.06016	0.559
62DAP/57DAP	1.08884	0.767
68DAP/62DAP	0.90861	0.543
68DAP/14DAP	0.42221	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.51718	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.71478	0.058
Mature Green Tomato/Ripe Tomato	11.052	0.015
Immature Eggplant/Mature Eggplant	0.33908	0.062
Ripe Pepper/Ripe Tomato	13.9201	0.256
Mature Eggplant/Ripe Tomato	13.4256	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.76644
12-2/M82	N/A	N/A
12-4/M82	0.8443
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	1.00265
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.18518
4-3/M82	1.02675
5-3/M82	2.21605
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	1.03029

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.6003
IL2-6/WTpooled	0.79519
IL7-5/WTpooled	1.12766	0.792
IL7-3/WTpooled	1.20647	1
IL12-4/WTpooled	0.92621	0.71
IL1-4/WTpooled	1.53829	1
WT/WTpooled	0.9731	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	0.97566	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92053
DC3000/delta hrp 6h	0.97633	0.95
DC3000/delta hrp 12h	0.90566	1
DC3000/delta hrp 24h	0.91662	0.513

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60856	0.057
DC3000 delta B/DC3000 delta AB	0.46436	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97029	1
Var 0h	1.13095	0.936
Var 12h I row2-row1	0.97523	0.565
Var 12h NI row2-row1	0.97496	0.713
Var 36h I row2-row1	0.93855	0.805
Var 36h NI row2-row1	0.90351	0.478
Var 60h I row2-row1	1.24042	0.543
Var 60h NI row2-row1	1.02605	0.904
Time course 0hI-0hNI	1.00189	1
Time course 12hI-12hNI	0.95488	0.49
Time course 36hI-36hNI	0.97486	0.366
Time course 60hI-60hNI	0.61495	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)	1.05815	0.921
transgenic ySAMdc/azygous control (breaker)	4.16563	0.162
transgenic ySAMdc/azygous control (red)	1.17367	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.5426	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.94651	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	21.4898	0.083
Manapal/WT (break)	12.5414	0.123
Manapal/WT (red)	2.3549	0.413