Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23883	0.244
27DAP/17DAP	0.45122	0.029
39DAP/27DAP	0.75053	0.286
41DAP/39DAP	0.67206	0.121
42DAP/41DAP	0.80044	1
43DAP/42DAP	1.09825	0.993
47DAP/43DAP	0.45649	0.049
52DAP/47DAP	0.679	0.168
57DAP/52DAP	1.02163	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40519	0.047
17DAP/reference	1.2704	0.457
27DAP/reference	1.05661	0.822
39DAP/reference	0.73413	0.085
41DAP/reference	0.59	0.016
42DAP/reference	0.66842	0.001
43DAP/reference	0.48092	0.015
47DAP/reference	0.29337	0.001
52DAP/reference	0.2531	0.012
57DAP/reference	0.36645	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60358	0.036
27DAP/17DAP	0.74428	0.339
39DAP/27DAP	0.50809	0.029
41DAP/39DAP	1.56309	0.012
42DAP/41DAP	0.72764	0.01
43DAP/42DAP	0.63749	0.022
47DAP/43DAP	0.93148	0.29
52DAP/47DAP	0.97607	0.907
57DAP/52DAP	1.11707	0.659
57DAP/7DAP	0.40692	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.82358	0.024
17DAP/reference	1.30084	0.008
27DAP/reference	1.02125	1
39DAP/reference	0.90224	0.23
41DAP/reference	0.56345	0.012
42DAP/reference	0.46734	0.01
43DAP/reference	0.51412	0.011
47DAP/reference	0.46877	0.03
52DAP/reference	0.80217	0.077
57DAP/reference	0.84482	0.097

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94107	0.503
17DAP/reference	0.91689	0.326
27DAP/reference	1.01911	0.642
39DAP/reference	0.69191	0.008
41DAP/reference	0.81046	0.073
42DAP/reference	0.78103	0.03
43DAP/reference	0.60205	0.022
47DAP/reference	0.94955	0.328
52DAP/reference	0.42059	0.003
57DAP/reference	0.40146	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.59534	0.015
17DAP/reference	2.83998	0.07
27DAP/reference	2.43817	0.013
39DAP/reference	1.74796	0.008
41DAP/reference	1.37608	0.045
42DAP/reference	0.85967	0.287
43DAP/reference	0.86724	0.179
47DAP/reference	0.56902	0.004
52DAP/reference	0.61337	0.122
57DAP/reference	1.37063	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.3404	0.966
26DAP/20DAP	0.84376	0.512
34DAP/26DAP	0.82302	0.237
51DAP/34DAP	0.73534	0.061
52DAP/51DAP	0.97252	1
53DAP/52DAP	1.25446	0.678
55DAP/53DAP	1.08496	0.608
57DAP/55DAP	1.02546	1
62DAP/57DAP	0.97552	0.994
68DAP/62DAP	0.86566	0.609
68DAP/14DAP	0.65869	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.85061	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09806	0.666
Mature Green Tomato/Ripe Tomato	6.42253	0.015
Immature Eggplant/Mature Eggplant	1.02946	0.683
Ripe Pepper/Ripe Tomato	3.26618	0.256
Mature Eggplant/Ripe Tomato	4.51776	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.64873
12-2/M82	0.43684	0.656
12-4/M82	0.88879	0.619
1-3/M82	1.69731
2-1-1/M82	N/A	N/A
2-1/M82	0.56327
2-6/M82	1.64973
3-2/M82	1.77008
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	1.92334	0.496
6-2/M82	2.53464
6-3/M82	N/A	N/A
7-1/M82	1.10915	0.87
7-2/M82	1.41539
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06445	0.493
IL2-6/WTpooled	1.4316	0.456
IL7-5/WTpooled	1.21613	0.792
IL7-3/WTpooled	1.05619	1
IL12-4/WTpooled	1.10771	0.695
IL1-4/WTpooled	0.954	1
WT/WTpooled	0.89879	0.873

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	0.83741	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98641	1
DC3000/delta hrp 6h	0.97556
DC3000/delta hrp 12h	0.74774	1
DC3000/delta hrp 24h	0.94865	0.629

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	0.40495	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95021	1
Exp 36h	0.96587	0.943
Exp 60h	0.75101	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97708	1
Var 0h	1.14068	0.782
Var 12h I row2-row1	1.00739	1
Var 12h NI row2-row1	0.8755	0.627
Var 36h I row2-row1	0.92177	1
Var 36h NI row2-row1	1.10607	1
Var 60h I row2-row1	1.67502	1
Var 60h NI row2-row1	1.03675	1
Time course 0hI-0hNI	1.00912	0.867
Time course 12hI-12hNI	1.04498	0.611
Time course 36hI-36hNI	1.11515	0.08
Time course 60hI-60hNI	0.63861	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)	1.17576	0.748
transgenic ySAMdc/azygous control (breaker)	3.8386	0.172
transgenic ySAMdc/azygous control (red)	2.1202	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8583	0.277

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.531	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.12169	0.088
Manapal/WT (break)	9.43516	0.13
Manapal/WT (red)	8.18263	0.15