Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25101	0.443
27DAP/17DAP	1.14578	0.845
39DAP/27DAP	1.10111	0.692
41DAP/39DAP	0.82182	0.322
42DAP/41DAP	0.95488	1
43DAP/42DAP	1.05497	1
47DAP/43DAP	1.22393	0.463
52DAP/47DAP	0.78858	0.488
57DAP/52DAP	1.13292	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2856	0.038
17DAP/reference	0.9898	0.904
27DAP/reference	1.07409	0.529
39DAP/reference	0.95269	0.527
41DAP/reference	1.20425	0.221
42DAP/reference	1.23286	0.001
43DAP/reference	0.91338	0.17
47DAP/reference	1.14054	0.004
52DAP/reference	1.44829	0.008
57DAP/reference	1.02753	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96309	0.679
27DAP/17DAP	1.06972	0.9
39DAP/27DAP	0.90373	0.132
41DAP/39DAP	1.18959	0.753
42DAP/41DAP	1.07704	0.916
43DAP/42DAP	1.02458	1
47DAP/43DAP	1.03751	0.934
52DAP/47DAP	0.86673	0.66
57DAP/52DAP	0.93279	0.564
57DAP/7DAP	0.7986

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15564	0.227
17DAP/reference	0.93446	0.253
27DAP/reference	0.99591	0.698
39DAP/reference	0.86487	0.031
41DAP/reference	0.95094	0.271
42DAP/reference	0.87086	0.2
43DAP/reference	0.92052	0.166
47DAP/reference	0.9369	0.383
52DAP/reference	0.8176	0.038
57DAP/reference	0.83412	0.08

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14242	0.206
17DAP/reference	1.32326	0.009
27DAP/reference	1.20304	0.107
39DAP/reference	1.1844	0.116
41DAP/reference	1.18311	0.234
42DAP/reference	1.5475	0.009
43DAP/reference	1.15892	0.192
47DAP/reference	1.22431	0.008
52DAP/reference	1.25001	0.114
57DAP/reference	1.30375	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10239	0.588
17DAP/reference	1.15839	0.326
27DAP/reference	1.02579	0.834
39DAP/reference	0.90287	0.092
41DAP/reference	1.03321	0.984
42DAP/reference	1.02994	0.816
43DAP/reference	1.14205	0.599
47DAP/reference	1.1478	0.228
52DAP/reference	1.29046	0.102
57DAP/reference	1.25163	0.147

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9505	1
26DAP/20DAP	1.29182	0.471
34DAP/26DAP	0.8034	0.067
51DAP/34DAP	1.29866	0.293
52DAP/51DAP	0.92582	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.15568	0.719
57DAP/55DAP	1.18685	0.805
62DAP/57DAP	1.03127	0.622
68DAP/62DAP	0.83544	0.464
68DAP/14DAP	0.99386	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.84278	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14165	0.058
Mature Green Tomato/Ripe Tomato	1.30843	0.363
Immature Eggplant/Mature Eggplant	0.84529	0.329
Ripe Pepper/Ripe Tomato	2.33765	1
Mature Eggplant/Ripe Tomato	6.22902	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78203	0.613
1-1-2/M82	1.12587	1
12-2/M82	0.78102	0.74
12-4/M82	1.09984	1
1-3/M82	N/A	N/A
2-1-1/M82	0.96233
2-1/M82	N/A	N/A
2-6/M82	1.12686	0.594
3-2/M82	1.09279	0.717
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.91217
4-3/M82	1.35143
5-3/M82	1.20999	0.572
6-2/M82	1.51911
6-3/M82	0.95141	1
7-1/M82	0.75538
7-2/M82	1.6213
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.44897
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86849
IL12-4/WTpooled	0.82035	0.71
IL1-4/WTpooled	1.07279	1
WT/WTpooled	1.57166	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	1.02858	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91595	0.839
DC3000/delta hrp 6h	1.09661	1
DC3000/delta hrp 12h	1.03133	1
DC3000/delta hrp 24h	1.01149	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98069	1
DC3000 delta B/DC3000 delta AB	1.00559	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98256	1
Var 0h	0.72765	1
Var 12h I row2-row1	0.86665	0.514
Var 12h NI row2-row1	0.93861	0.906
Var 36h I row2-row1	1.20605	0.601
Var 36h NI row2-row1	0.95561	0.706
Var 60h I row2-row1	0.86901	0.306
Var 60h NI row2-row1	0.89501	0.69
Time course 0hI-0hNI	0.9821	0.961
Time course 12hI-12hNI	1.03267	0.693
Time course 36hI-36hNI	1.07631	0.19
Time course 60hI-60hNI	1.08095	0.16

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)	0.82433	0.314
transgenic ySAMdc/azygous control (breaker)	0.67936	0.137
transgenic ySAMdc/azygous control (red)	1.06857	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93055	0.048

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.50687	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07162	0.307
Manapal/WT (break)	1.20731	1
Manapal/WT (red)	0.9051	0.503