Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98983	0.743
27DAP/17DAP	1.01613	1
39DAP/27DAP	1.18184	0.765
41DAP/39DAP	1.03222	0.873
42DAP/41DAP	1.26387	0.691
43DAP/42DAP	1.05511	1
47DAP/43DAP	1.21405	0.444
52DAP/47DAP	0.95797	0.832
57DAP/52DAP	1.35543	0.771

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26165	0.028
17DAP/reference	0.9734	0.701
27DAP/reference	1.0917	0.831
39DAP/reference	1.14223	0.144
41DAP/reference	1.22764	0.122
42DAP/reference	1.32499	0.016
43DAP/reference	1.43787
47DAP/reference	1.32088	0.034
52DAP/reference	1.11478	0.141
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93994	0.509
27DAP/17DAP	1.00595	0.969
39DAP/27DAP	1.05421	0.587
41DAP/39DAP	1.15091	0.336
42DAP/41DAP	0.94251	0.439
43DAP/42DAP	0.96053	0.597
47DAP/43DAP	1.0973	0.581
52DAP/47DAP	0.87689	0.382
57DAP/52DAP	0.86952	0.375
57DAP/7DAP	0.95876	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88303	0.115
17DAP/reference	0.81308	0.014
27DAP/reference	0.84851	0.01
39DAP/reference	0.84112	0.012
41DAP/reference	0.79757	0.014
42DAP/reference	0.80449	0.014
43DAP/reference	0.78013	0.017
47DAP/reference	0.90422	0.293
52DAP/reference	0.77147	0.126
57DAP/reference	0.752	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24088	0.063
17DAP/reference	1.31757	0.028
27DAP/reference	1.40783	0.04
39DAP/reference	1.16818	0.146
41DAP/reference	1.15379	0.204
42DAP/reference	1.2282	0.057
43DAP/reference	1.40849	0.026
47DAP/reference	1.22188	0.011
52DAP/reference	1.33026	0.013
57DAP/reference	1.4193	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94238	0.362
17DAP/reference	1.15605	0.294
27DAP/reference	0.81692	0.027
39DAP/reference	0.84941	0.069
41DAP/reference	0.89344	0.077
42DAP/reference	0.92839	0.445
43DAP/reference	1.04241	1
47DAP/reference	1.04947	0.792
52DAP/reference	0.90736	0.36
57DAP/reference	0.7653	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04915	1
26DAP/20DAP	0.89662	0.317
34DAP/26DAP	1.02149	1
51DAP/34DAP	0.80019	0.305
52DAP/51DAP	0.82154	0.151
53DAP/52DAP	0.94697	0.803
55DAP/53DAP	0.79821	0.088
57DAP/55DAP	1.11711	0.694
62DAP/57DAP	1.07051	1
68DAP/62DAP	0.65059	0.211
68DAP/14DAP	0.77009	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25679	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.45457	0.081
Mature Green Tomato/Ripe Tomato	1.2319	0.437
Immature Eggplant/Mature Eggplant	1.98653	0.05
Ripe Pepper/Ripe Tomato	6.33658	1
Mature Eggplant/Ripe Tomato	5.48624	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.04351	1
12-2/M82	N/A	N/A
12-4/M82	1.07645
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.99346
4-3/M82	N/A	N/A
5-3/M82	1.57583	0.427
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.01327	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81423	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.9511	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.93013	0.834
WT/WTpooled	N/A	N/A

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	1.0702	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07899	0.921
DC3000/delta hrp 6h	0.93381	0.95
DC3000/delta hrp 12h	1.18745	1
DC3000/delta hrp 24h	0.37807	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11944	0.556
DC3000 delta B/DC3000 delta AB	1.06788	0.524

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99299	1
Exp 36h	0.78299	0.471
Exp 60h	0.82946	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00672	1
Var 0h	0.99166	1
Var 12h I row2-row1	1.02544	0.692
Var 12h NI row2-row1	1.0008	1
Var 36h I row2-row1	1.08336	1
Var 36h NI row2-row1	0.79326	0.645
Var 60h I row2-row1	1.23525	0.562
Var 60h NI row2-row1	1.04522	0.904
Time course 0hI-0hNI	1.01115	1
Time course 12hI-12hNI	0.99638	1
Time course 36hI-36hNI	0.8505	0.089
Time course 60hI-60hNI	0.65641	0.007

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)	0.63072	0.297
transgenic ySAMdc/azygous control (breaker)	0.75295	0.173
transgenic ySAMdc/azygous control (red)	0.89469	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95738	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28795	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19289	0.307
Manapal/WT (break)	1.18411	1
Manapal/WT (red)	1.57492	0.164