Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.20.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68167	0.373
27DAP/17DAP	0.8002	0.589
39DAP/27DAP	0.91735	0.631
41DAP/39DAP	0.91677	0.6
42DAP/41DAP	1.04992	1
43DAP/42DAP	1.26337	1
47DAP/43DAP	1.32463	0.727
52DAP/47DAP	1.4394	0.593
57DAP/52DAP	0.63786	0.681

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03238	1
17DAP/reference	1.09901	0.011
27DAP/reference	1.04315	0.794
39DAP/reference	0.96527	0.68
41DAP/reference	1.13981	0.48
42DAP/reference	1.02896	0.485
43DAP/reference	0.82775
47DAP/reference	1.15418	0.728
52DAP/reference	1.023	0.548
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95062	0.644
27DAP/17DAP	1.22794	0.928
39DAP/27DAP	0.70195	0.198
41DAP/39DAP	0.96032	0.959
42DAP/41DAP	1.13002	1
43DAP/42DAP	1.14435	0.324
47DAP/43DAP	1.35908	0.5
52DAP/47DAP	0.91966	0.801
57DAP/52DAP	1.00247	1
57DAP/7DAP	0.68321

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25368	0.082
17DAP/reference	1.82597	0.007
27DAP/reference	1.56717	0.007
39DAP/reference	2.12093	0.005
41DAP/reference	2.08807	0.013
42DAP/reference	1.88253	0.006
43DAP/reference	2.27312	0.007
47DAP/reference	1.40378	0.318
52DAP/reference	1.6943	0.01
57DAP/reference	1.86558	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11095	0.36
17DAP/reference	0.96446	0.447
27DAP/reference	1.13596	0.875
39DAP/reference	0.89491	0.243
41DAP/reference	0.71712	0.03
42DAP/reference	1.13907	0.759
43DAP/reference	0.92082	0.45
47DAP/reference	1.0786	0.589
52DAP/reference	0.97214	0.407
57DAP/reference	1.00541	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45329	0.021
17DAP/reference	1.23794	0.531
27DAP/reference	2.06209	0.02
39DAP/reference	1.68952	0.01
41DAP/reference	1.62709	0.018
42DAP/reference	1.3873	0.028
43DAP/reference	1.53686	0.089
47DAP/reference	0.94145	0.357
52DAP/reference	1.38002	0.186
57DAP/reference	1.62466	0.648

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96383	1
26DAP/20DAP	2.13784	0.39
34DAP/26DAP	0.94871	0.961
51DAP/34DAP	0.95863
52DAP/51DAP	1.19856	0.358
53DAP/52DAP	0.96667	0.803
55DAP/53DAP	1.15009	0.994
57DAP/55DAP	0.94337	0.539
62DAP/57DAP	0.96333	0.994
68DAP/62DAP	1.21592	0.515
68DAP/14DAP	1.97771	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20627	0.496

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74916	0.23
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.99098	1
Ripe Pepper/Ripe Tomato	2.99117
Mature Eggplant/Ripe Tomato	8.39837

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
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	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88116	0.321
IL2-6/WTpooled	1.11279	0.456
IL7-5/WTpooled	1.16373	0.792
IL7-3/WTpooled	0.79736	0.418
IL12-4/WTpooled	1.00459	1
IL1-4/WTpooled	1.01519	0.426
WT/WTpooled	0.91499	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	1.22999	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.78804	0.942
DC3000/delta hrp 12h	1.13469	1
DC3000/delta hrp 24h	1.08212

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.30366	1
Exp 36h	1.70339	1
Exp 60h	1.32601	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93615	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.94542	0.856
Var 12h NI row2-row1	0.98684	1
Var 36h I row2-row1	1.14764	0.742
Var 36h NI row2-row1	3.39414	1
Var 60h I row2-row1	0.83122	0.285
Var 60h NI row2-row1	0.80031	0.756
Time course 0hI-0hNI	1.0563	0.603
Time course 12hI-12hNI	1.1988	0.201
Time course 36hI-36hNI	1.33554	0.035
Time course 60hI-60hNI	2.98621	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)	1.15306	0.384
transgenic ySAMdc/azygous control (breaker)	0.7471	0.142
transgenic ySAMdc/azygous control (red)	0.87208	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00386	0.854

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)	0.8914	1
Manapal/WT (break)	1.0986	1
Manapal/WT (red)	0.95311	0.863