Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43714	0.017
27DAP/17DAP	0.46263	0.036
39DAP/27DAP	1.09383	0.769
41DAP/39DAP	0.46045	0.041
42DAP/41DAP	0.75481	0.774
43DAP/42DAP	1.09529	1
47DAP/43DAP	0.83363	0.484
52DAP/47DAP	0.76249	0.479
57DAP/52DAP	1.08176	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19471	0.01
17DAP/reference	1.754	0.014
27DAP/reference	2.0604	0.01
39DAP/reference	0.66145	0.01
41DAP/reference	0.61679	0.009
42DAP/reference	0.7645	0.004
43DAP/reference	0.65498	0.019
47DAP/reference	0.61085	0.001
52DAP/reference	0.59167	0.019
57DAP/reference	0.87116	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.25787	0.026
27DAP/17DAP	2.29387	0.022
39DAP/27DAP	0.3678	0.028
41DAP/39DAP	0.38494	0.013
42DAP/41DAP	0.90649	0.469
43DAP/42DAP	1.20138	0.056
47DAP/43DAP	0.68394	0.008
52DAP/47DAP	1.00123	0.97
57DAP/52DAP	0.85712	0.082
57DAP/7DAP	0.14098	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.90133	0.026
17DAP/reference	0.98964	0.518
27DAP/reference	0.92294	0.171
39DAP/reference	1.11649	0.033
41DAP/reference	0.96609	0.449
42DAP/reference	0.94561	0.371
43DAP/reference	1.09368	0.511
47DAP/reference	0.95128	0.504
52DAP/reference	0.91894	0.163
57DAP/reference	0.96561	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66008	0.181
17DAP/reference	1.71553	0.022
27DAP/reference	1.34652	0.288
39DAP/reference	0.55546	0.012
41DAP/reference	0.72545	0.016
42DAP/reference	1.07563	0.879
43DAP/reference	0.60022	0.007
47DAP/reference	0.57806	0.011
52DAP/reference	0.51612	0.004
57DAP/reference	0.45131	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47975	0.019
17DAP/reference	1.4677	0.118
27DAP/reference	1.22805	0.325
39DAP/reference	0.86915	0.122
41DAP/reference	0.96454	0.512
42DAP/reference	0.93443	0.445
43DAP/reference	0.90026	0.334
47DAP/reference	0.40999	0.004
52DAP/reference	0.69471	0.125
57DAP/reference	0.68672	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98626	1
26DAP/20DAP	1.53758
34DAP/26DAP	0.68834	0.093
51DAP/34DAP	0.543	0.078
52DAP/51DAP	1.07511	0.431
53DAP/52DAP	0.73235	0.069
55DAP/53DAP	0.56074	0.019
57DAP/55DAP	0.48123	0.031
62DAP/57DAP	1.05604
68DAP/62DAP	1.48273	0.657
68DAP/14DAP	0.35608	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.28119	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.6952	0.058
Mature Green Tomato/Ripe Tomato	8.97061	0.015
Immature Eggplant/Mature Eggplant	0.32133	0.058
Ripe Pepper/Ripe Tomato	37.8369	0.256
Mature Eggplant/Ripe Tomato	50.8268	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2106	0.742
1-1-2/M82	1.03488	1
12-2/M82	N/A	N/A
12-4/M82	0.92789	1
1-3/M82	0.61938
2-1-1/M82	0.71291
2-1/M82	N/A	N/A
2-6/M82	1.01342	1
3-2/M82	0.73437
4-1-1/M82	0.5893
4-1/M82	1.01826	1
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.97969	1
6-2/M82	N/A	N/A
6-3/M82	0.86989	0.715
7-1/M82	N/A	N/A
7-2/M82	0.89971
9-3-2/M82	0.86815	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.13329	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.70634	0.31
IL12-4/WTpooled	0.82182	0.71
IL1-4/WTpooled	0.82858
WT/WTpooled	1.08369	0.785

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	0.74478	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92055	1
DC3000/delta hrp 6h	1.14253	1
DC3000/delta hrp 12h	1.16651	1
DC3000/delta hrp 24h	0.76713	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54883	0.023
DC3000 delta B/DC3000 delta AB	0.48752	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06174	1
Exp 36h	0.7461	0.471
Exp 60h	0.69349	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01009	1
Var 0h	1.35808	0.594
Var 12h I row2-row1	0.84705	0.363
Var 12h NI row2-row1	0.96	0.906
Var 36h I row2-row1	1.11106	0.742
Var 36h NI row2-row1	1.12298	1
Var 60h I row2-row1	0.89573	0.832
Var 60h NI row2-row1	1.07626	1
Time course 0hI-0hNI	1.05349	0.719
Time course 12hI-12hNI	0.95895	0.761
Time course 36hI-36hNI	0.87597	0.026
Time course 60hI-60hNI	0.24908	0.006

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)	0.75505	0.324
transgenic ySAMdc/azygous control (breaker)	3.45311	0.248
transgenic ySAMdc/azygous control (red)	0.85526	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.71289	0.065

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	5.45469	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.68258	0.09
Manapal/WT (break)	2.10706	1
Manapal/WT (red)	1.14689	1