Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.15.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92128	0.445
27DAP/17DAP	1.38127	0.633
39DAP/27DAP	0.96833	0.682
41DAP/39DAP	1.6224	0.58
42DAP/41DAP	1.0274	1
43DAP/42DAP	0.79682	0.713
47DAP/43DAP	1.38116	0.474
52DAP/47DAP	1.16192	0.776
57DAP/52DAP	1.06761	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06858	0.872
17DAP/reference	1.52235	0.017
27DAP/reference	1.2913	0.024
39DAP/reference	1.28262	0.162
41DAP/reference	1.58082	0.013
42DAP/reference	1.51932	0.001
43DAP/reference	1.17686	0.36
47DAP/reference	1.28131	0.011
52DAP/reference	1.12921	0.607
57DAP/reference	0.93763	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04284	0.934
27DAP/17DAP	1.08992	0.852
39DAP/27DAP	0.97082	0.804
41DAP/39DAP	0.9676	0.968
42DAP/41DAP	0.88064	0.214
43DAP/42DAP	0.88888	0.101
47DAP/43DAP	0.91288	0.31
52DAP/47DAP	1.26282	0.471
57DAP/52DAP	1.05473	0.997
57DAP/7DAP	0.94802	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87972	0.138
17DAP/reference	0.924	0.22
27DAP/reference	0.85884	0.058
39DAP/reference	0.88126	0.198
41DAP/reference	0.89208	0.107
42DAP/reference	0.89906	0.211
43DAP/reference	0.84854	0.086
47DAP/reference	1.00362	1
52DAP/reference	0.90465	0.254
57DAP/reference	0.89411	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15153	0.495
17DAP/reference	1.64957	0.008
27DAP/reference	1.36426	0.071
39DAP/reference	1.27906	0.029
41DAP/reference	1.2806	0.157
42DAP/reference	1.20727	0.07
43DAP/reference	1.5587	0.009
47DAP/reference	1.32535	0.027
52DAP/reference	1.31644	0.011
57DAP/reference	1.35713	0.172

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00339	0.804
17DAP/reference	1.18386	0.665
27DAP/reference	0.95641	0.376
39DAP/reference	1.06867	0.792
41DAP/reference	0.93801	0.293
42DAP/reference	1.06102	0.994
43DAP/reference	1.19576	0.418
47DAP/reference	1.3617	0.05
52DAP/reference	1.0497	0.888
57DAP/reference	1.0704	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97856	1
26DAP/20DAP	0.96367	1
34DAP/26DAP	0.9715	1
51DAP/34DAP	1.50993	0.978
52DAP/51DAP	0.87056	1
53DAP/52DAP	0.82796	0.587
55DAP/53DAP	1.07294	1
57DAP/55DAP	0.95953	0.688
62DAP/57DAP	0.87509	0.871
68DAP/62DAP	0.74194	0.263
68DAP/14DAP	0.76768	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91845	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71989	0.238
Mature Green Tomato/Ripe Tomato	1.06558	1
Immature Eggplant/Mature Eggplant	0.66352	0.07
Ripe Pepper/Ripe Tomato	0.80453	1
Mature Eggplant/Ripe Tomato	0.86556	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.23246	0.536
1-1-2/M82	1.06854	0.977
12-2/M82	0.82768
12-4/M82	0.83162	1
1-3/M82	0.87719	0.378
2-1-1/M82	0.88244
2-1/M82	0.97676
2-6/M82	1.0556
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.97486
4-3-2/M82	0.70352
4-3/M82	0.60208
5-3/M82	0.99242	1
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	1.15502
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.73978
IL1-4/WTpooled	1.23674	1
WT/WTpooled	0.75324

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	1.03432	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98939	1
DC3000/delta hrp 6h	1.0097	0.95
DC3000/delta hrp 12h	1.08991	1
DC3000/delta hrp 24h	1.04791	0.604

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14974	1
Exp 36h	0.86494	0.82
Exp 60h	1.17685	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94855	1
Var 0h	1.13248	0.98
Var 12h I row2-row1	0.93113	0.77
Var 12h NI row2-row1	1.01513	1
Var 36h I row2-row1	0.89807	1
Var 36h NI row2-row1	0.88328
Var 60h I row2-row1	0.93636	0.582
Var 60h NI row2-row1	0.79433	0.932
Time course 0hI-0hNI	1.04638	0.662
Time course 12hI-12hNI	0.99764	1
Time course 36hI-36hNI	1.15383	0.019
Time course 60hI-60hNI	1.35962	0.096

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)	0.91677	0.306
transgenic ySAMdc/azygous control (breaker)	0.89815	0.173
transgenic ySAMdc/azygous control (red)	1.02165	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94543	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77888	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09866	1
Manapal/WT (break)	0.82087	0.333
Manapal/WT (red)	0.92436	0.424