Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.20.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35861	0.588
27DAP/17DAP	1.22783	0.828
39DAP/27DAP	0.69509	0.338
41DAP/39DAP	1.64773	0.293
42DAP/41DAP	0.98057	1
43DAP/42DAP	1.02643	0.937
47DAP/43DAP	1.33351	0.42
52DAP/47DAP	1.04619	0.991
57DAP/52DAP	1.09092	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84447	0.326
17DAP/reference	1.64629
27DAP/reference	0.94791	0.61
39DAP/reference	1.43766
41DAP/reference	0.67652	0.016
42DAP/reference	0.61624
43DAP/reference	N/A	N/A
47DAP/reference	N/A	N/A
52DAP/reference	N/A	N/A
57DAP/reference	0.71931	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.58081	0.036
27DAP/17DAP	1.08263	0.924
39DAP/27DAP	1.10275	0.581
41DAP/39DAP	1.06151	1
42DAP/41DAP	0.96585	0.7
43DAP/42DAP	0.95933	0.684
47DAP/43DAP	1.01488	0.956
52DAP/47DAP	1.06592	0.823
57DAP/52DAP	1.32035	0.679
57DAP/7DAP	0.34922

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58885	0.031
17DAP/reference	1.72663	0.009
27DAP/reference	1.64888	0.011
39DAP/reference	1.13964	0.96
41DAP/reference	1.21955	0.121
42DAP/reference	1.23111	0.046
43DAP/reference	1.78219	0.048
47DAP/reference	1.04934	1
52DAP/reference	1.70631	0.021
57DAP/reference	1.64547	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85209	0.248
17DAP/reference	0.71192	0.007
27DAP/reference	0.85442	0.393
39DAP/reference	0.93362	0.348
41DAP/reference	0.84067	0.137
42DAP/reference	4.37001	0.342
43DAP/reference	0.74324	0.06
47DAP/reference	0.65796
52DAP/reference	0.82779	0.031
57DAP/reference	0.84835	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45704	0.025
17DAP/reference	1.08612	0.665
27DAP/reference	2.01533	0.025
39DAP/reference	1.51771	0.406
41DAP/reference	1.40795	0.069
42DAP/reference	1.55943	0.023
43DAP/reference	1.75786	0.059
47DAP/reference	0.98164	0.525
52DAP/reference	1.58587	0.059
57DAP/reference	1.2453	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14397	1
26DAP/20DAP	1.03486	1
34DAP/26DAP	1.46677	0.819
51DAP/34DAP	1.06025	0.719
52DAP/51DAP	1.1915	0.596
53DAP/52DAP	0.95756	0.797
55DAP/53DAP	1.33414	0.898
57DAP/55DAP	1.37883	0.865
62DAP/57DAP	0.93379	0.871
68DAP/62DAP	1.83723	0.523
68DAP/14DAP	1.94436	0.033

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13616	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9717	0.826
Mature Green Tomato/Ripe Tomato	0.82386	0.2
Immature Eggplant/Mature Eggplant	1.41265	0.057
Ripe Pepper/Ripe Tomato	0.61721	0.224
Mature Eggplant/Ripe Tomato	0.76962	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98968
1-1-2/M82	0.83399
12-2/M82	N/A	N/A
12-4/M82	0.92345	1
1-3/M82	1.09408
2-1-1/M82	1.13073
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.01339
4-1-1/M82	1.60285
4-1/M82	1.28262
4-3-2/M82	0.70402	0.487
4-3/M82	0.79672	1
5-3/M82	1.02594	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.94964
7-2/M82	1.14458	1
9-3-2/M82	0.8481	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96001	1
IL2-6/WTpooled	1.30394	0.427
IL7-5/WTpooled	1.07855	1
IL7-3/WTpooled	0.85636
IL12-4/WTpooled	0.94116	1
IL1-4/WTpooled	1.0846	1
WT/WTpooled	0.9615	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	1.58093	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01624	0.921
DC3000/delta hrp 6h	0.87183	0.95
DC3000/delta hrp 12h	0.97695	1
DC3000/delta hrp 24h	1.00577	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.91126	0.042
DC3000 delta B/DC3000 delta AB	2.67621	0.032

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88363	1
Exp 36h	1.01619	0.943
Exp 60h	0.9852	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00425	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.39634	0.379
Var 12h NI row2-row1	1.15053	1
Var 36h I row2-row1	0.92787	1
Var 36h NI row2-row1	1.26772	0.482
Var 60h I row2-row1	0.97689	1
Var 60h NI row2-row1	1.01773	1
Time course 0hI-0hNI	0.85798	0.151
Time course 12hI-12hNI	1.0174	1
Time course 36hI-36hNI	0.90273	0.19
Time course 60hI-60hNI	0.70561	0.047

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)	1.10652	0.384
transgenic ySAMdc/azygous control (breaker)	0.92729	0.49
transgenic ySAMdc/azygous control (red)	0.91511	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03225	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.42856	0.09
Manapal/WT (break)	1.40927	0.14
Manapal/WT (red)	1.79427	0.164