Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04484	0.851
27DAP/17DAP	1.32488	0.688
39DAP/27DAP	0.90441	0.544
41DAP/39DAP	1.08193	0.663
42DAP/41DAP	1.00451	1
43DAP/42DAP	0.98995	0.932
47DAP/43DAP	1.27842	0.444
52DAP/47DAP	0.9532	0.843
57DAP/52DAP	1.00858	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94844	0.39
17DAP/reference	1.05719	0.148
27DAP/reference	1.05735	0.258
39DAP/reference	1.04906	0.679
41DAP/reference	1.0922	0.145
42DAP/reference	0.92581	0.027
43DAP/reference	1.01199	1
47DAP/reference	0.97451	0.345
52DAP/reference	0.94149	0.341
57DAP/reference	0.90313	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98219	0.732
27DAP/17DAP	0.99409	0.943
39DAP/27DAP	1.0512	0.626
41DAP/39DAP	0.9858	0.997
42DAP/41DAP	1.01458	0.936
43DAP/42DAP	1.02036	0.585
47DAP/43DAP	1.0158	0.926
52DAP/47DAP	1.02283	0.915
57DAP/52DAP	1.00246	0.929
57DAP/7DAP	1.11832	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94196	0.27
17DAP/reference	0.93821	0.064
27DAP/reference	0.88148	0.014
39DAP/reference	0.97723	0.307
41DAP/reference	0.95604	0.166
42DAP/reference	0.9591	0.275
43DAP/reference	0.88162	0.029
47DAP/reference	0.88869	0.168
52DAP/reference	0.94123	0.254
57DAP/reference	0.95942	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90203	0.087
17DAP/reference	0.93909	0.077
27DAP/reference	0.85724	0.139
39DAP/reference	0.84774	0.105
41DAP/reference	0.8743	0.127
42DAP/reference	0.91801	0.261
43DAP/reference	0.97359	0.569
47DAP/reference	0.97399	0.473
52DAP/reference	0.94445	0.203
57DAP/reference	1.11797	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92513	0.158
17DAP/reference	0.95434	0.292
27DAP/reference	0.90376	0.052
39DAP/reference	0.96142	0.299
41DAP/reference	0.90989	0.032
42DAP/reference	0.83678	0.087
43DAP/reference	0.93292	0.025
47DAP/reference	1.0108	1
52DAP/reference	1.05924	0.614
57DAP/reference	0.8112	0.073

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00733	0.966
26DAP/20DAP	0.98839	1
34DAP/26DAP	1.06723	0.819
51DAP/34DAP	0.8066	0.259
52DAP/51DAP	0.93693	1
53DAP/52DAP	1.08696	0.565
55DAP/53DAP	0.99585	0.917
57DAP/55DAP	1.11885	0.525
62DAP/57DAP	1.14685	0.833
68DAP/62DAP	1.01419	0.939
68DAP/14DAP	0.96807	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91984	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04831	0.287
Mature Green Tomato/Ripe Tomato	0.9483	0.569
Immature Eggplant/Mature Eggplant	1.45987	0.054
Ripe Pepper/Ripe Tomato	1.61471	0.258
Mature Eggplant/Ripe Tomato	1.81211	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96076	0.944
1-1-2/M82	0.86335	1
12-2/M82	0.96972	0.955
12-4/M82	0.8777	1
1-3/M82	0.92943	0.378
2-1-1/M82	1.03419	1
2-1/M82	1.39626	0.345
2-6/M82	0.99744	1
3-2/M82	0.92017	1
4-1-1/M82	0.99398	1
4-1/M82	0.71333	1
4-3-2/M82	1.02548	1
4-3/M82	0.98395	1
5-3/M82	0.99077	1
6-2/M82	0.95526	1
6-3/M82	1.0256	1
7-1/M82	1.1364	1
7-2/M82	0.96749	0.881
9-3-2/M82	0.95266	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.5938	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.82367
IL12-4/WTpooled	0.86512	1
IL1-4/WTpooled	1.01713	1
WT/WTpooled	1.18512	0.957

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	0.79738	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04623	0.692
DC3000/delta hrp 6h	1.41779	0.95
DC3000/delta hrp 12h	0.92148	1
DC3000/delta hrp 24h	1.00128	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13439	0.134
DC3000 delta B/DC3000 delta AB	1.13326	0.304

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	1.06679	1
Var 0h	0.91811	0.933
Var 12h I row2-row1	1.14929	0.379
Var 12h NI row2-row1	0.91632	0.713
Var 36h I row2-row1	0.76294	0.805
Var 36h NI row2-row1	0.91754	0.706
Var 60h I row2-row1	1.48726	1
Var 60h NI row2-row1	1.24007	0.904
Time course 0hI-0hNI	1.09362	0.63
Time course 12hI-12hNI	1.04414	0.77
Time course 36hI-36hNI	0.96296	0.426
Time course 60hI-60hNI	1.83017	0.053

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)	0.99523	0.931
transgenic ySAMdc/azygous control (breaker)	1.73185	0.178
transgenic ySAMdc/azygous control (red)	1.20026	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00661	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82435	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.57808	0.172
Manapal/WT (break)	0.73842	0.299
Manapal/WT (red)	1.12243	0.413