Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.7327	0.045
27DAP/17DAP	0.91789	0.817
39DAP/27DAP	1.14575	0.841
41DAP/39DAP	0.80358	0.322
42DAP/41DAP	0.84211	1
43DAP/42DAP	1.04603	1
47DAP/43DAP	0.93495	0.71
52DAP/47DAP	1.18819	0.886
57DAP/52DAP	1.04977	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80016	0.094
17DAP/reference	0.80831	0.111
27DAP/reference	0.86087	0.257
39DAP/reference	0.90869	0.404
41DAP/reference	0.92828	0.434
42DAP/reference	1.00813	0.665
43DAP/reference	0.99181	0.763
47DAP/reference	1.07469	0.243
52DAP/reference	0.87726	0.244
57DAP/reference	0.94908	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13893	0.356
27DAP/17DAP	1.15212	0.482
39DAP/27DAP	0.84081	0.181
41DAP/39DAP	1.14241	0.763
42DAP/41DAP	0.98124	0.762
43DAP/42DAP	0.98741	0.854
47DAP/43DAP	0.96333	0.75
52DAP/47DAP	1.00197	0.987
57DAP/52DAP	1.00922	0.869
57DAP/7DAP	1.13377	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46407	0.042
17DAP/reference	1.42574	0.007
27DAP/reference	1.44421	0.007
39DAP/reference	1.36184	0.006
41DAP/reference	1.21997	0.077
42DAP/reference	1.32261	0.037
43DAP/reference	1.36941	0.008
47DAP/reference	1.16688	0.081
52DAP/reference	1.16902	0.308
57DAP/reference	1.18493	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75354	0.14
17DAP/reference	0.92488	0.434
27DAP/reference	1.15508	0.629
39DAP/reference	1.133	0.62
41DAP/reference	1.08438	0.318
42DAP/reference	1.10413	0.476
43DAP/reference	0.71281	0.015
47DAP/reference	1.11703	0.388
52DAP/reference	0.89487	0.029
57DAP/reference	0.59671	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12057	0.356
17DAP/reference	0.92591	0.433
27DAP/reference	1.3167	0.035
39DAP/reference	1.38384	0.038
41DAP/reference	1.18027	0.093
42DAP/reference	1.3922	0.049
43DAP/reference	1.13065	0.439
47DAP/reference	0.8375	0.08
52DAP/reference	1.20506	0.335
57DAP/reference	1.22232	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16918	0.966
26DAP/20DAP	1.24233	0.334
34DAP/26DAP	0.98075	0.98
51DAP/34DAP	0.90247	0.466
52DAP/51DAP	0.91341	1
53DAP/52DAP	1.08209	0.413
55DAP/53DAP	0.84963	0.489
57DAP/55DAP	1.06604	0.935
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.89835	0.834
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43392	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.20643	0.176
Mature Green Tomato/Ripe Tomato	2.00226	0.053
Immature Eggplant/Mature Eggplant	1.14781	0.215
Ripe Pepper/Ripe Tomato	1.10166	1
Mature Eggplant/Ripe Tomato	0.96327	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82679	0.736
1-1-2/M82	1.04106	1
12-2/M82	0.84316	0.955
12-4/M82	1.05924	1
1-3/M82	3.22421	0.248
2-1-1/M82	0.97122	1
2-1/M82	0.65662	0.345
2-6/M82	0.79856	1
3-2/M82	1.70389
4-1-1/M82	0.92156	1
4-1/M82	1.18296	1
4-3-2/M82	1.72228	0.284
4-3/M82	1.0934	1
5-3/M82	0.9612	1
6-2/M82	1.2037
6-3/M82	1.01304	1
7-1/M82	0.95092	1
7-2/M82	1.16395	1
9-3-2/M82	1.38361

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.6393
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.03851	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16131	0.823
DC3000/delta hrp 6h	1.00072	0.95
DC3000/delta hrp 12h	1.0123	1
DC3000/delta hrp 24h	0.97551	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13029
DC3000 delta B/DC3000 delta AB	1.05361	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12197	1
Exp 36h	1.14181	1
Exp 60h	1.19866	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.82253	0.933
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.00912	0.921
transgenic ySAMdc/azygous control (breaker)	0.60103	0.131
transgenic ySAMdc/azygous control (red)	0.82531	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28967	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.56043	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.57961	0.172
Manapal/WT (break)	0.7359	0.333
Manapal/WT (red)	0.76314	0.181