Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.15.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11466	0.725
27DAP/17DAP	1.00938	1
39DAP/27DAP	1.14155	0.779
41DAP/39DAP	1.42645	0.212
42DAP/41DAP	1.09809	0.997
43DAP/42DAP	0.89298	0.613
47DAP/43DAP	0.88852	0.595
52DAP/47DAP	1.87856	0.23
57DAP/52DAP	0.75423	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31753	0.038
17DAP/reference	1.2629	0.014
27DAP/reference	1.06874	0.539
39DAP/reference	1.08339	0.545
41DAP/reference	1.32312	0.025
42DAP/reference	1.25389	0.001
43DAP/reference	1.10924	0.306
47DAP/reference	1.23482	0.004
52DAP/reference	1.28966	0.027
57DAP/reference	1.10641	0.392

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0213	1
27DAP/17DAP	1.12086	0.694
39DAP/27DAP	1.06839	0.548
41DAP/39DAP	1.02491	0.896
42DAP/41DAP	1.0036	0.926
43DAP/42DAP	0.9867	0.928
47DAP/43DAP	1.01603	0.963
52DAP/47DAP	1.00767	0.97
57DAP/52DAP	1.04647	0.971
57DAP/7DAP	1.07994	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84311	0.066
17DAP/reference	0.87431	0.082
27DAP/reference	0.86305	0.037
39DAP/reference	0.79497	0.015
41DAP/reference	0.90534	0.174
42DAP/reference	0.92861	0.178
43DAP/reference	0.74374	0.011
47DAP/reference	1.10093	0.965
52DAP/reference	0.83367	0.028
57DAP/reference	0.7518	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98442	0.831
17DAP/reference	1.36573	0.068
27DAP/reference	1.33585	0.025
39DAP/reference	1.25732	0.059
41DAP/reference	1.23968	0.255
42DAP/reference	1.32523	0.012
43DAP/reference	1.27426	0.135
47DAP/reference	1.27475	0.016
52DAP/reference	1.39427	0.006
57DAP/reference	1.49193	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9517	0.422
17DAP/reference	1.03031	0.988
27DAP/reference	0.86963	0.102
39DAP/reference	0.89807	0.222
41DAP/reference	0.94077	0.417
42DAP/reference	1.07314	0.635
43DAP/reference	1.01936	0.796
47DAP/reference	1.31091	0.196
52DAP/reference	0.86856	0.351
57DAP/reference	1.50975	0.157

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03522	1
26DAP/20DAP	0.93923	1
34DAP/26DAP	1.05703	1
51DAP/34DAP	0.95146	0.667
52DAP/51DAP	1.04962	0.676
53DAP/52DAP	1.06933	0.819
55DAP/53DAP	1.17711	0.634
57DAP/55DAP	1.21242	0.311
62DAP/57DAP	1.08695	0.935
68DAP/62DAP	0.93272	0.722
68DAP/14DAP	0.72605	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.28352	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.90577	0.446
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02335	1
1-1-2/M82	0.92841	1
12-2/M82	1.23801	0.519
12-4/M82	0.73274
1-3/M82	0.92021	0.286
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.96813	1
3-2/M82	0.9267
4-1-1/M82	0.86718
4-1/M82	1.34813
4-3-2/M82	0.84025	1
4-3/M82	0.68653
5-3/M82	0.87583	0.49
6-2/M82	0.81475
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.00667	1
9-3-2/M82	0.7626

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.03184
IL2-6/WTpooled	1.14555	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.72611	0.418
IL12-4/WTpooled	0.96326	1
IL1-4/WTpooled	1.13616	1
WT/WTpooled	1.08267	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	1.01712	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02256	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.12884	1
DC3000/delta hrp 24h	1.13783	0.158

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86361	0.882
DC3000 delta B/DC3000 delta AB	0.80718	0.134

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02353	1
Exp 36h	N/A	N/A
Exp 60h	0.93772	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03595	1
Var 0h	0.46026	1
Var 12h I row2-row1	1.07488	0.202
Var 12h NI row2-row1	0.88235	0.546
Var 36h I row2-row1	0.80664	0.805
Var 36h NI row2-row1	1.10416	1
Var 60h I row2-row1	1.29079	0.562
Var 60h NI row2-row1	1.22647	0.904
Time course 0hI-0hNI	1.02045	0.852
Time course 12hI-12hNI	1.05776	0.65
Time course 36hI-36hNI	0.99603	0.753
Time course 60hI-60hNI	1.15682	0.011

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)	1.17196	0.312
transgenic ySAMdc/azygous control (breaker)	1.05222	1
transgenic ySAMdc/azygous control (red)	1.1081	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94731	0.146

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11661	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82474	1
Manapal/WT (break)	0.88579	1
Manapal/WT (red)	0.87091	0.607