Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.9.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10994	0.755
27DAP/17DAP	0.5293	0.04
39DAP/27DAP	0.64728	0.512
41DAP/39DAP	0.69105	0.068
42DAP/41DAP	0.56051	0.397
43DAP/42DAP	0.97382	0.912
47DAP/43DAP	0.62364	0.101
52DAP/47DAP	0.92101	0.634
57DAP/52DAP	0.92153	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71686	0.052
17DAP/reference	0.69042	0.057
27DAP/reference	0.70685	0.059
39DAP/reference	0.60916	0.027
41DAP/reference	0.59433	0.026
42DAP/reference	0.63763	0.001
43DAP/reference	0.78601	0.148
47DAP/reference	0.65478	0.001
52DAP/reference	0.51189	0.015
57DAP/reference	0.76917	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52801	0.041
27DAP/17DAP	0.81431	0.446
39DAP/27DAP	0.47818	0.029
41DAP/39DAP	1.18919	0.135
42DAP/41DAP	0.8143	0.045
43DAP/42DAP	0.65941	0.022
47DAP/43DAP	1.03495	0.973
52DAP/47DAP	0.95266	0.753
57DAP/52DAP	1.03409	0.877
57DAP/7DAP	0.45842	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28084	0.093
17DAP/reference	1.11027	0.199
27DAP/reference	0.94799	0.375
39DAP/reference	0.57488	0.011
41DAP/reference	0.4953	0.009
42DAP/reference	0.52667	0.01
43DAP/reference	0.51262	0.01
47DAP/reference	0.41734	0.03
52DAP/reference	0.4848	0.012
57DAP/reference	0.46697	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60549	0.016
17DAP/reference	0.48615	0.005
27DAP/reference	0.61644	0.026
39DAP/reference	0.59482	0.029
41DAP/reference	0.80556	0.038
42DAP/reference	0.63209	0.011
43DAP/reference	0.37683	0.002
47DAP/reference	0.64669	0.011
52DAP/reference	0.37862	0.003
57DAP/reference	0.34118	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.08096	0.015
17DAP/reference	1.73311	0.206
27DAP/reference	1.41478	0.029
39DAP/reference	1.17704	0.163
41DAP/reference	0.86745	0.119
42DAP/reference	0.8066	0.059
43DAP/reference	0.64434	0.032
47DAP/reference	0.56403	0.004
52DAP/reference	0.86668	0.351
57DAP/reference	1.04568	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19547	0.916
26DAP/20DAP	1.11486	0.66
34DAP/26DAP	1.01724	1
51DAP/34DAP	0.62243	0.053
52DAP/51DAP	0.89143	1
53DAP/52DAP	0.81925	0.177
55DAP/53DAP	0.6674	0.052
57DAP/55DAP	1.41262	0.643
62DAP/57DAP	1.05491	0.994
68DAP/62DAP	1.11532	0.754
68DAP/14DAP	0.94553	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37396	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.50517	0.058
Mature Green Tomato/Ripe Tomato	15.3435	0.015
Immature Eggplant/Mature Eggplant	0.3724	0.058
Ripe Pepper/Ripe Tomato	3.87761	1
Mature Eggplant/Ripe Tomato	4.73946	1

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	0.82538	0.619
1-3/M82	N/A	N/A
2-1-1/M82	1.09978
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	0.80581	0.72
5-3/M82	0.86164	0.387
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.88357	1
7-2/M82	0.99909
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.54048	0.277
IL2-6/WTpooled	0.6588	0.383
IL7-5/WTpooled	1.32479	0.792
IL7-3/WTpooled	1.25861	0.362
IL12-4/WTpooled	1.16739	0.695
IL1-4/WTpooled	0.87151	0.457
WT/WTpooled	1.01014	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	1.00476	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00191	1
DC3000/delta hrp 6h	0.89797	0.95
DC3000/delta hrp 12h	0.82774	1
DC3000/delta hrp 24h	0.52654	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50448	0.027
DC3000 delta B/DC3000 delta AB	0.56388	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97793	1
Exp 36h	0.86766	0.699
Exp 60h	0.90097	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95779	1
Var 0h	1.03433	1
Var 12h I row2-row1	1.15657	0.613
Var 12h NI row2-row1	0.96727	0.713
Var 36h I row2-row1	1.09649	1
Var 36h NI row2-row1	0.93189	0.549
Var 60h I row2-row1	1.63489	0.562
Var 60h NI row2-row1	1.04508	1
Time course 0hI-0hNI	0.98079	0.94
Time course 12hI-12hNI	1.14723	0.051
Time course 36hI-36hNI	1.16039	0.355
Time course 60hI-60hNI	0.41399	0.015

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)	1.18978	0.571
transgenic ySAMdc/azygous control (breaker)	2.43785	0.165
transgenic ySAMdc/azygous control (red)	1.08672	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.5416	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.48503	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.06103	0.083
Manapal/WT (break)	5.20092	0.123
Manapal/WT (red)	2.18034	0.413