Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.19.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05604	0.891
27DAP/17DAP	0.82302	0.539
39DAP/27DAP	1.8966	0.217
41DAP/39DAP	0.80033	0.306
42DAP/41DAP	1.22725	0.933
43DAP/42DAP	0.879	0.783
47DAP/43DAP	0.62247	0.105
52DAP/47DAP	1.18049	0.876
57DAP/52DAP	1.07546	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32473	0.03
17DAP/reference	1.30935	0.089
27DAP/reference	1.26497	0.033
39DAP/reference	1.30734	0.039
41DAP/reference	1.32003	0.036
42DAP/reference	1.51507	0.001
43DAP/reference	1.14547	0.095
47DAP/reference	1.54152	0.001
52DAP/reference	1.43614	0.027
57DAP/reference	1.40063	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79026	0.044
27DAP/17DAP	1.04806	0.771
39DAP/27DAP	1.01182	0.862
41DAP/39DAP	1.10122	0.837
42DAP/41DAP	0.94864	0.599
43DAP/42DAP	0.91774	0.157
47DAP/43DAP	1.08051	0.5
52DAP/47DAP	0.83843	0.099
57DAP/52DAP	1.0584	0.732
57DAP/7DAP	0.84277	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98677	0.613
17DAP/reference	0.91142	0.389
27DAP/reference	1.22962	0.073
39DAP/reference	1.34616	0.073
41DAP/reference	1.42849	0.019
42DAP/reference	1.13533	0.233
43DAP/reference	1.02606	0.665
47DAP/reference	1.108	1
52DAP/reference	1.10144	0.781
57DAP/reference	1.07393	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81539	0.129
17DAP/reference	1.1976	0.426
27DAP/reference	1.12376	0.48
39DAP/reference	1.23378	0.15
41DAP/reference	1.25276	0.086
42DAP/reference	1.3708	0.012
43DAP/reference	1.08379	0.809
47DAP/reference	1.41237	0.02
52DAP/reference	1.49177	0.018
57DAP/reference	1.08406	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11102	0.505
17DAP/reference	1.08892	0.317
27DAP/reference	0.93323	0.286
39DAP/reference	1.16782	0.296
41DAP/reference	1.18085	0.637
42DAP/reference	1.22249	0.097
43DAP/reference	1.38923	0.049
47DAP/reference	1.10219	0.48
52DAP/reference	1.39625	0.165
57DAP/reference	1.41513	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.341	0.966
26DAP/20DAP	1.29478	0.357
34DAP/26DAP	1.03059	1
51DAP/34DAP	0.90755	0.611
52DAP/51DAP	1.13484	0.431
53DAP/52DAP	0.95863	0.797
55DAP/53DAP	0.92667	0.663
57DAP/55DAP	1.04575	0.96
62DAP/57DAP	0.95827	0.871
68DAP/62DAP	1.00575	0.81
68DAP/14DAP	0.93774	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.3489	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.33283	0.038
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.60789
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.31515
12-2/M82	N/A	N/A
12-4/M82	1.28527	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.14426
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.80767
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.78667
7-2/M82	1.46709
9-3-2/M82	1.11619	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70898	0.321
IL2-6/WTpooled	0.78445	1
IL7-5/WTpooled	1.15677	1
IL7-3/WTpooled	0.8279	0.31
IL12-4/WTpooled	0.81441	0.71
IL1-4/WTpooled	0.79159	0.394
WT/WTpooled	0.94552	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	1.25137	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91016	1
DC3000/delta hrp 6h	0.88055
DC3000/delta hrp 12h	0.71477
DC3000/delta hrp 24h	0.75028	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99455
DC3000 delta B/DC3000 delta AB	1.11171	0.335

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	1.0188	1
Var 0h	0.91093	0.933
Var 12h I row2-row1	1.06091	1
Var 12h NI row2-row1	1.30316	0.649
Var 36h I row2-row1	0.99288	1
Var 36h NI row2-row1	0.90299	0.706
Var 60h I row2-row1	0.78044	0.374
Var 60h NI row2-row1	0.80068	0.329
Time course 0hI-0hNI	0.93318	0.615
Time course 12hI-12hNI	1.05686	0.684
Time course 36hI-36hNI	1.59084	0.007
Time course 60hI-60hNI	1.96905	0.008

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)	0.8146	0.299
transgenic ySAMdc/azygous control (breaker)	0.83253	0.49
transgenic ySAMdc/azygous control (red)	0.91896	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04905	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72392	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1703	1
Manapal/WT (break)	1.05536	1
Manapal/WT (red)	1.00938	1