Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.11.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1012	0.646
27DAP/17DAP	1.23539	0.742
39DAP/27DAP	1.07524	0.944
41DAP/39DAP	0.9145	0.678
42DAP/41DAP	1.14883	0.929
43DAP/42DAP	0.86434	0.761
47DAP/43DAP	1.29931	0.455
52DAP/47DAP	0.93499	0.662
57DAP/52DAP	1.20856	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03336	0.9
17DAP/reference	1.08568	0.08
27DAP/reference	1.04068	0.66
39DAP/reference	1.04196	0.514
41DAP/reference	1.15548	0.287
42DAP/reference	0.97525	0.348
43DAP/reference	1.04166	0.73
47DAP/reference	0.99038	0.568
52DAP/reference	0.91745	0.058
57DAP/reference	1.0704	0.366

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47145	0.036
27DAP/17DAP	1.00876	0.969
39DAP/27DAP	1.3297	0.079
41DAP/39DAP	0.97192	0.968
42DAP/41DAP	0.96011	0.69
43DAP/42DAP	0.75524	0.206
47DAP/43DAP	1.00654	1
52DAP/47DAP	0.83815	0.203
57DAP/52DAP	0.69345	0.136
57DAP/7DAP	0.85662

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8609	0.129
17DAP/reference	0.8588	0.014
27DAP/reference	0.93104	0.062
39DAP/reference	0.92477	0.17
41DAP/reference	0.8049	0.04
42DAP/reference	0.85068	0.014
43DAP/reference	0.84178	0.038
47DAP/reference	0.99108	0.671
52DAP/reference	0.68913	0.012
57DAP/reference	0.74885	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00771	0.993
17DAP/reference	0.90847	0.058
27DAP/reference	1.03933	0.86
39DAP/reference	1.00466	0.682
41DAP/reference	0.99418	0.57
42DAP/reference	1.02826	1
43DAP/reference	1.00049	0.787
47DAP/reference	1.19913	0.009
52DAP/reference	0.9575	0.351
57DAP/reference	1.00459	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.808	0.031
17DAP/reference	1.00347	0.751
27DAP/reference	0.86982	0.058
39DAP/reference	0.83607	0.017
41DAP/reference	0.82598	0.028
42DAP/reference	0.85564	0.017
43DAP/reference	0.85119	0.017
47DAP/reference	0.95723	0.465
52DAP/reference	1.05329	0.724
57DAP/reference	1.17891	0.157

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05354	0.966
26DAP/20DAP	0.84143	0.183
34DAP/26DAP	0.97816	0.972
51DAP/34DAP	0.63073	0.06
52DAP/51DAP	1.02914	1
53DAP/52DAP	1.03499	0.895
55DAP/53DAP	1.13157	0.629
57DAP/55DAP	1.11141	0.865
62DAP/57DAP	1.11646	0.569
68DAP/62DAP	1.23165	0.737
68DAP/14DAP	0.92224	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.06579	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.16133	0.331
Immature Eggplant/Mature Eggplant	1.58882	0.05
Ripe Pepper/Ripe Tomato	0.16325	0.224
Mature Eggplant/Ripe Tomato	1.37769	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02987
1-1-2/M82	1.16773	1
12-2/M82	0.45315
12-4/M82	1.4095	1
1-3/M82	1.47228
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.07752	0.695
3-2/M82	1.34304
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.73419
4-3/M82	1.25896	1
5-3/M82	1.91488	0.572
6-2/M82	N/A	N/A
6-3/M82	0.52448	0.857
7-1/M82	1.2312	0.539
7-2/M82	N/A	N/A
9-3-2/M82	1.27268

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.22203	0.277
IL2-6/WTpooled	1.0363	0.659
IL7-5/WTpooled	1.0921	0.792
IL7-3/WTpooled	0.99234	1
IL12-4/WTpooled	1.02954	0.891
IL1-4/WTpooled	0.91905	0.834
WT/WTpooled	1.06154	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04311	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.06939	1
DC3000/delta hrp 24h	0.9091	0.534

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.43922
DC3000 delta B/DC3000 delta AB	0.74559

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	1.02593	1
Var 0h	1.21358	0.259
Var 12h I row2-row1	1.12334	0.228
Var 12h NI row2-row1	0.62376	0.627
Var 36h I row2-row1	0.91017	0.805
Var 36h NI row2-row1	0.40835	1
Var 60h I row2-row1	0.91937	0.285
Var 60h NI row2-row1	0.57565	0.932
Time course 0hI-0hNI	0.94869	0.758
Time course 12hI-12hNI	0.98271	0.893
Time course 36hI-36hNI	1.16911	0.722
Time course 60hI-60hNI	1.57666	0.115

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)	0.63831	0.286
transgenic ySAMdc/azygous control (breaker)	0.86377	0.173
transgenic ySAMdc/azygous control (red)	0.83322	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95163	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27224	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.03062	0.088
Manapal/WT (break)	1.06123	1
Manapal/WT (red)	0.9304	0.728