Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.6.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92831	0.558
27DAP/17DAP	0.99892	1
39DAP/27DAP	1.8263	0.073
41DAP/39DAP	0.52117	0.045
42DAP/41DAP	1.01056	1
43DAP/42DAP	1.01138	0.937
47DAP/43DAP	0.8204	0.407
52DAP/47DAP	0.83423	0.557
57DAP/52DAP	1.56539	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60219	0.024
17DAP/reference	0.9015	0.079
27DAP/reference	0.8142	0.015
39DAP/reference	1.22262	0.368
41DAP/reference	0.98246	0.667
42DAP/reference	1.54991	0.001
43DAP/reference	2.53392	0.007
47DAP/reference	2.87642	0.001
52DAP/reference	1.06702	0.73
57DAP/reference	1.86567	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27437	0.096
27DAP/17DAP	1.01048	1
39DAP/27DAP	0.86563	0.074
41DAP/39DAP	1.10898	0.781
42DAP/41DAP	0.895	0.269
43DAP/42DAP	0.80592	0.024
47DAP/43DAP	1.07468	0.713
52DAP/47DAP	0.89553	0.304
57DAP/52DAP	0.88111	0.349
57DAP/7DAP	0.53328	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64647	0.085
17DAP/reference	1.53139	0.007
27DAP/reference	2.02444	0.008
39DAP/reference	2.06679	0.006
41DAP/reference	1.65272	0.021
42DAP/reference	2.39156	0.009
43DAP/reference	1.66398	0.006
47DAP/reference	1.23794	0.404
52DAP/reference	2.3762	0.007
57DAP/reference	2.01415	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65627	0.012
17DAP/reference	0.79564	0.03
27DAP/reference	0.73133	0.018
39DAP/reference	0.7133	0.04
41DAP/reference	0.70418	0.015
42DAP/reference	0.80578	0.039
43DAP/reference	0.79701	0.036
47DAP/reference	0.79305	0.009
52DAP/reference	0.71342	0.009
57DAP/reference	0.78387	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30392	0.146
17DAP/reference	0.98136	0.636
27DAP/reference	1.53333	0.035
39DAP/reference	1.63007	0.05
41DAP/reference	1.46935	0.12
42DAP/reference	1.68417	0.008
43DAP/reference	1.67743	0.013
47DAP/reference	2.2517	0.005
52DAP/reference	1.94296	0.121
57DAP/reference	0.85793	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04747	0.966
26DAP/20DAP	1.7094	0.453
34DAP/26DAP	1.45215	0.819
51DAP/34DAP	0.94865	0.77
52DAP/51DAP	0.7114	0.151
53DAP/52DAP	0.84379	0.311
55DAP/53DAP	0.74247	0.08
57DAP/55DAP	1.02646	0.997
62DAP/57DAP	1.09357	0.723
68DAP/62DAP	1.67993	1
68DAP/14DAP	0.7048	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.48349	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.49433
Mature Green Tomato/Ripe Tomato	2.03706	0.015
Immature Eggplant/Mature Eggplant	1.10234	0.311
Ripe Pepper/Ripe Tomato	0.27492	0.293
Mature Eggplant/Ripe Tomato	1.73532	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.77168
1-1-2/M82	1.32042	1
12-2/M82	0.81618	0.535
12-4/M82	0.97435
1-3/M82	1.92595
2-1-1/M82	1.08509	1
2-1/M82	N/A	N/A
2-6/M82	1.0672	0.695
3-2/M82	0.97869
4-1-1/M82	N/A	N/A
4-1/M82	0.89299
4-3-2/M82	1.6186	0.241
4-3/M82	1.28676	1
5-3/M82	1.20135	0.572
6-2/M82	N/A	N/A
6-3/M82	0.809	1
7-1/M82	N/A	N/A
7-2/M82	1.20646
9-3-2/M82	1.44569	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75905	1
IL2-6/WTpooled	0.90552	0.348
IL7-5/WTpooled	1.79698
IL7-3/WTpooled	0.89047	1
IL12-4/WTpooled	1.19232	0.532
IL1-4/WTpooled	1.00136	1
WT/WTpooled	0.99827	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	1.00904	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08045	0.914
DC3000/delta hrp 6h	1.01896
DC3000/delta hrp 12h	1.17386	1
DC3000/delta hrp 24h	1.01579	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.4837	0.134
DC3000 delta B/DC3000 delta AB	1.35324	0.349

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11468	1
Exp 36h	2.4915	0.489
Exp 60h	1.55836	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09009
Var 0h	1.07112	1
Var 12h I row2-row1	1.02837	0.736
Var 12h NI row2-row1	1.11171	1
Var 36h I row2-row1	0.90375	1
Var 36h NI row2-row1	0.88412	0.645
Var 60h I row2-row1	0.91609	0.952
Var 60h NI row2-row1	0.789	0.306
Time course 0hI-0hNI	0.90975	0.338
Time course 12hI-12hNI	1.0462	0.63
Time course 36hI-36hNI	1.15254	0.401
Time course 60hI-60hNI	1.44754	0.025

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)	0.89409	0.338
transgenic ySAMdc/azygous control (breaker)	1.12574	0.178
transgenic ySAMdc/azygous control (red)	0.93098	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03419	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7814	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67484	0.172
Manapal/WT (break)	0.92559	1
Manapal/WT (red)	1.0879	1