Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.19.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01711	0.964
27DAP/17DAP	0.97443	0.99
39DAP/27DAP	0.93837	0.67
41DAP/39DAP	1.48016	0.31
42DAP/41DAP	1.14328	1
43DAP/42DAP	0.83201	0.643
47DAP/43DAP	0.82937	0.473
52DAP/47DAP	1.94136	0.204
57DAP/52DAP	0.77186	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05052	0.824
17DAP/reference	1.28163	0.132
27DAP/reference	1.13008	1
39DAP/reference	1.37345	0.017
41DAP/reference	2.27592	0.013
42DAP/reference	1.20102	0.043
43DAP/reference	1.03911
47DAP/reference	1.06463	0.306
52DAP/reference	1.15318	0.766
57DAP/reference	0.65129	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99486	0.826
27DAP/17DAP	1.08453	0.712
39DAP/27DAP	0.96064	0.721
41DAP/39DAP	1.02203	0.921
42DAP/41DAP	1.01316	0.929
43DAP/42DAP	1.18314	0.112
47DAP/43DAP	0.98092	0.933
52DAP/47DAP	1.05232	0.823
57DAP/52DAP	1.01071	1
57DAP/7DAP	1.02214

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7996	0.08
17DAP/reference	0.77568	0.016
27DAP/reference	0.803	0.011
39DAP/reference	0.80157	0.011
41DAP/reference	0.7873	0.019
42DAP/reference	0.78875	0.014
43DAP/reference	0.7276	0.014
47DAP/reference	0.90719	0.383
52DAP/reference	0.71508	0.017
57DAP/reference	0.7527	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03029	0.915
17DAP/reference	1.26386	0.257
27DAP/reference	1.16071	0.292
39DAP/reference	1.28616	0.077
41DAP/reference	1.19906	0.099
42DAP/reference	1.34084	0.01
43DAP/reference	1.29141	0.104
47DAP/reference	1.16177	0.051
52DAP/reference	1.28949	0.024
57DAP/reference	1.32326	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8872	0.147
17DAP/reference	1.09337	0.641
27DAP/reference	0.92208	0.319
39DAP/reference	0.87387	0.122
41DAP/reference	0.87877	0.046
42DAP/reference	0.88947	0.22
43DAP/reference	0.91602	0.294
47DAP/reference	1.24464	0.585
52DAP/reference	0.61471	0.071
57DAP/reference	0.98641	0.652

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15049	1
26DAP/20DAP	1.03072	0.931
34DAP/26DAP	1.08962	1
51DAP/34DAP	0.90897	0.498
52DAP/51DAP	0.98218	1
53DAP/52DAP	0.95253	0.79
55DAP/53DAP	1.05028	0.922
57DAP/55DAP	1.00373	0.953
62DAP/57DAP	1.17582	0.515
68DAP/62DAP	0.97003	0.834
68DAP/14DAP	0.87134	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.52402	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.61044	0.107
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.4799
Mature Eggplant/Ripe Tomato	0.66577	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9892	0.708
1-1-2/M82	0.83847	0.958
12-2/M82	1.10004	1
12-4/M82	1.03301	1
1-3/M82	0.88415	0.441
2-1-1/M82	1.00365	1
2-1/M82	1.21423	1
2-6/M82	1.03364	1
3-2/M82	N/A	N/A
4-1-1/M82	1.21759	0.968
4-1/M82	1.09643	1
4-3-2/M82	0.67254	0.487
4-3/M82	0.9209
5-3/M82	1.01846	1
6-2/M82	0.83001
6-3/M82	0.84324	0.857
7-1/M82	1.07196	1
7-2/M82	0.94378	1
9-3-2/M82	0.84586

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.57097
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.08854

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	0.83105	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98492	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.14291	1
DC3000/delta hrp 24h	1.06922	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54696	0.024
DC3000 delta B/DC3000 delta AB	0.59174	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	1.01813	1
Var 0h	1.19615	0.782
Var 12h I row2-row1	0.86086	0.39
Var 12h NI row2-row1	0.92901	0.713
Var 36h I row2-row1	0.981	1
Var 36h NI row2-row1	1.19746	0.482
Var 60h I row2-row1	1.24066	0.562
Var 60h NI row2-row1	1.05225	0.904
Time course 0hI-0hNI	1.01838	1
Time course 12hI-12hNI	0.95304	0.618
Time course 36hI-36hNI	0.86366	0.051
Time course 60hI-60hNI	0.37559	0.006

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)	1.38094	0.931
transgenic ySAMdc/azygous control (breaker)	1.06767	1
transgenic ySAMdc/azygous control (red)	0.87513	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89523	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.39364	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.74409	0.183