Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.13.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03555	0.961
27DAP/17DAP	0.97628	0.975
39DAP/27DAP	1.46414	0.134
41DAP/39DAP	0.71106	0.119
42DAP/41DAP	1.26868	0.672
43DAP/42DAP	1.24759	0.985
47DAP/43DAP	1.07182	0.538
52DAP/47DAP	0.86552	0.662
57DAP/52DAP	0.9987	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04185	0.662
17DAP/reference	1.14842	0.092
27DAP/reference	1.16053	0.139
39DAP/reference	1.28872	0.083
41DAP/reference	1.22429	0.085
42DAP/reference	1.26549	0.003
43DAP/reference	1.21543	0.044
47DAP/reference	1.35035	0.001
52DAP/reference	0.99178	0.618
57DAP/reference	1.09547	0.22

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08022	0.642
27DAP/17DAP	1.29479	0.164
39DAP/27DAP	0.82122	0.167
41DAP/39DAP	1.18876	0.895
42DAP/41DAP	0.97632	0.753
43DAP/42DAP	1.11136	0.324
47DAP/43DAP	0.93198	0.577
52DAP/47DAP	0.92904	0.746
57DAP/52DAP	0.90804	0.418
57DAP/7DAP	0.86649	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.82578	0.026
17DAP/reference	1.41966	0.015
27DAP/reference	1.3373	0.014
39DAP/reference	1.3919	0.007
41DAP/reference	1.29285	0.041
42DAP/reference	1.46674	0.012
43DAP/reference	1.37998	0.007
47DAP/reference	1.79436	0.014
52DAP/reference	1.45602	0.018
57DAP/reference	1.31407	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1169	0.531
17DAP/reference	1.25402	0.01
27DAP/reference	1.36433	0.02
39DAP/reference	1.23543	0.063
41DAP/reference	0.89738	0.145
42DAP/reference	0.98485	0.534
43DAP/reference	0.8894	0.269
47DAP/reference	0.99433	0.643
52DAP/reference	0.99804	0.713
57DAP/reference	0.87681	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1475	0.329
17DAP/reference	1.04135	0.738
27DAP/reference	1.29294	0.042
39DAP/reference	1.35308	0.018
41DAP/reference	1.13001	0.077
42DAP/reference	1.32732	0.018
43DAP/reference	1.37638	0.026
47DAP/reference	1.03201	0.73
52DAP/reference	1.27779	0.077
57DAP/reference	1.27669	0.113

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86297	0.26
26DAP/20DAP	1.44266	0.541
34DAP/26DAP	1.0895	1
51DAP/34DAP	1.26284	0.171
52DAP/51DAP	0.7549	1
53DAP/52DAP	1.13774	0.343
55DAP/53DAP	0.78752	0.027
57DAP/55DAP	1.54694	0.584
62DAP/57DAP	0.81764	0.466
68DAP/62DAP	0.96533	0.787
68DAP/14DAP	0.86503

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42885	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07474	0.417
Mature Green Tomato/Ripe Tomato	1.59876
Immature Eggplant/Mature Eggplant	1.06714	0.259
Ripe Pepper/Ripe Tomato	1.07225	1
Mature Eggplant/Ripe Tomato	1.11272	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0346	0.551
1-1-2/M82	1.19611	1
12-2/M82	0.9614	0.955
12-4/M82	1.05281	1
1-3/M82	1.86505	0.26
2-1-1/M82	0.99365	1
2-1/M82	0.97894	0.74
2-6/M82	0.80475	1
3-2/M82	0.98497	1
4-1-1/M82	1.20568	1
4-1/M82	1.28355	0.853
4-3-2/M82	1.2473	0.253
4-3/M82	1.0066	1
5-3/M82	1.04498	1
6-2/M82	1.19505	1
6-3/M82	0.96867	1
7-1/M82	1.0246	1
7-2/M82	1.0445	1
9-3-2/M82	1.08994	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70825	0.243
IL2-6/WTpooled	1.11853	0.659
IL7-5/WTpooled	0.95389	1
IL7-3/WTpooled	0.81528	0.31
IL12-4/WTpooled	0.81946	0.581
IL1-4/WTpooled	0.91539	0.562
WT/WTpooled	0.94643	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	1.08368	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07721	0.914
DC3000/delta hrp 6h	0.92897	0.95
DC3000/delta hrp 12h	1.02546	1
DC3000/delta hrp 24h	1.31424	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14167	0.044
DC3000 delta B/DC3000 delta AB	1.18147	0.209

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19968	1
Exp 36h	1.24967	1
Exp 60h	1.26546	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00548	1
Var 0h	1.45593	0.594
Var 12h I row2-row1	0.93299	0.77
Var 12h NI row2-row1	1.03852	1
Var 36h I row2-row1	0.97799	1
Var 36h NI row2-row1	0.93228	0.549
Var 60h I row2-row1	0.96362	0.952
Var 60h NI row2-row1	0.87332	0.335
Time course 0hI-0hNI	1.00876	1
Time course 12hI-12hNI	0.97794	0.745
Time course 36hI-36hNI	1.17176	0.035
Time course 60hI-60hNI	2.35844	0.008

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)	1.08048	0.397
transgenic ySAMdc/azygous control (breaker)	0.96739	1
transgenic ySAMdc/azygous control (red)	0.88002	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17377	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02186	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73149	0.172
Manapal/WT (break)	0.70308	0.297
Manapal/WT (red)	0.66617	0.181