Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74459	0.125
27DAP/17DAP	1.19449	0.799
39DAP/27DAP	2.48417	0.025
41DAP/39DAP	1.04484	0.994
42DAP/41DAP	0.94635	1
43DAP/42DAP	1.36201	0.968
47DAP/43DAP	1.18765	0.448
52DAP/47DAP	1.45807	0.371
57DAP/52DAP	0.61694	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.74657	0.015
17DAP/reference	1.45137	0.012
27DAP/reference	2.09745	0.011
39DAP/reference	1.88867	0.023
41DAP/reference	1.89664	0.014
42DAP/reference	1.55118	0.001
43DAP/reference	1.79648	0.009
47DAP/reference	1.89244	0.001
52DAP/reference	1.22692	0.158
57DAP/reference	1.19515	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8183	0.148
27DAP/17DAP	1.34307	0.061
39DAP/27DAP	0.80422	0.085
41DAP/39DAP	0.74612	0.209
42DAP/41DAP	1.39249	0.172
43DAP/42DAP	1.18148	0.056
47DAP/43DAP	1.02308	0.973
52DAP/47DAP	0.85967	0.296
57DAP/52DAP	0.96687	0.7
57DAP/7DAP	1.10555	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04545	0.793
17DAP/reference	0.70722	0.011
27DAP/reference	0.85593	0.055
39DAP/reference	0.79249	0.013
41DAP/reference	0.77871	0.019
42DAP/reference	0.70408	0.013
43DAP/reference	0.77253	0.025
47DAP/reference	1.24892	0.149
52DAP/reference	0.84438	0.057
57DAP/reference	0.76836	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34761	0.43
17DAP/reference	1.7096	0.21
27DAP/reference	1.72472	0.019
39DAP/reference	1.52992	0.026
41DAP/reference	1.44308	0.015
42DAP/reference	1.43633	0.015
43DAP/reference	1.1242	0.522
47DAP/reference	1.1575	0.015
52DAP/reference	1.12921	0.322
57DAP/reference	0.93713	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18862	0.026
17DAP/reference	1.06726	0.72
27DAP/reference	0.94662	0.27
39DAP/reference	1.13801	0.13
41DAP/reference	1.19899	0.554
42DAP/reference	1.50597	0.03
43DAP/reference	2.12883	0.019
47DAP/reference	1.51486	0.14
52DAP/reference	1.39471	0.11
57DAP/reference	1.52168	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86928
26DAP/20DAP	2.10523	0.097
34DAP/26DAP	0.74561	0.177
51DAP/34DAP	1.32558	0.07
52DAP/51DAP	1.12367	0.313
53DAP/52DAP	0.57549	0.049
55DAP/53DAP	0.62932	0.023
57DAP/55DAP	1.37355	0.854
62DAP/57DAP	1.58512	0.081
68DAP/62DAP	0.71482	0.464
68DAP/14DAP	0.76225

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58978	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.24943	0.058
Mature Green Tomato/Ripe Tomato	0.37372	0.016
Immature Eggplant/Mature Eggplant	2.21638	0.05
Ripe Pepper/Ripe Tomato	0.57176	0.224
Mature Eggplant/Ripe Tomato	0.33157	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99163	1
1-1-2/M82	1.25716	1
12-2/M82	0.91644	0.862
12-4/M82	1.05147	1
1-3/M82	1.16097	1
2-1-1/M82	1.3274	0.3
2-1/M82	N/A	N/A
2-6/M82	1.27221	0.594
3-2/M82	1.08012
4-1-1/M82	1.07539	1
4-1/M82	1.55858	0.853
4-3-2/M82	2.03515	0.262
4-3/M82	2.02056	0.268
5-3/M82	0.96089	1
6-2/M82	1.35301
6-3/M82	1.00417	1
7-1/M82	0.93158	0.803
7-2/M82	1.36226	0.318
9-3-2/M82	1.79438	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1684	0.365
IL2-6/WTpooled	0.93749	1
IL7-5/WTpooled	2.09621
IL7-3/WTpooled	1.06844	1
IL12-4/WTpooled	0.88435	0.581
IL1-4/WTpooled	1.08181	1
WT/WTpooled	0.91833	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	0.94167	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95149	1
DC3000/delta hrp 6h	0.86785	0.95
DC3000/delta hrp 12h	1.08709	1
DC3000/delta hrp 24h	1.41609

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96784	0.803
DC3000 delta B/DC3000 delta AB	0.79594	0.114

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14262	1
Exp 36h	0.76235	0.471
Exp 60h	1.09288	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03517	1
Var 0h	1.12849	0.98
Var 12h I row2-row1	0.76355	0.338
Var 12h NI row2-row1	0.94124	0.82
Var 36h I row2-row1	1.05435	0.601
Var 36h NI row2-row1	1.20596	0.276
Var 60h I row2-row1	0.89237	0.306
Var 60h NI row2-row1	1.00422	1
Time course 0hI-0hNI	1.03702	0.852
Time course 12hI-12hNI	0.99783	1
Time course 36hI-36hNI	1.03001	1
Time course 60hI-60hNI	0.37106	0.006

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)	1.16115	0.297
transgenic ySAMdc/azygous control (breaker)	0.64282	0.251
transgenic ySAMdc/azygous control (red)	1.11379	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03234	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88679	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.10001	0.086
Manapal/WT (break)	1.98462	0.126
Manapal/WT (red)	2.96747	0.126