Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.60704	0.111
27DAP/17DAP	0.59902	0.072
39DAP/27DAP	1.31206	0.56
41DAP/39DAP	0.87754	0.563
42DAP/41DAP	0.68911	0.397
43DAP/42DAP	1.07096	1
47DAP/43DAP	0.65031	0.137
52DAP/47DAP	1.24024	0.645
57DAP/52DAP	0.89334	0.872

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36255	0.014
17DAP/reference	1.14866	0.355
27DAP/reference	1.10954	0.175
39DAP/reference	1.04837	0.691
41DAP/reference	0.89365	0.201
42DAP/reference	0.99385	0.517
43DAP/reference	0.91675	0.234
47DAP/reference	1.03634	0.773
52DAP/reference	0.77377	0.043
57DAP/reference	1.01946	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95823	0.644
27DAP/17DAP	0.69816	0.121
39DAP/27DAP	0.86331	0.123
41DAP/39DAP	0.77544	0.061
42DAP/41DAP	0.98845	0.777
43DAP/42DAP	0.93986	0.503
47DAP/43DAP	0.98984	0.939
52DAP/47DAP	1.23688	0.552
57DAP/52DAP	0.91104	0.608
57DAP/7DAP	0.48989	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.3954	0.03
17DAP/reference	4.42279	0.092
27DAP/reference	5.75424	0.006
39DAP/reference	6.82938	0.005
41DAP/reference	6.501	0.009
42DAP/reference	8.33459	0.006
43DAP/reference	9.89969	0.006
47DAP/reference	4.45868	0.178
52DAP/reference	7.7354	0.007
57DAP/reference	5.02936	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48291	0.141
17DAP/reference	1.43919	0.06
27DAP/reference	0.95986	0.467
39DAP/reference	1.14906	0.602
41DAP/reference	0.87717	0.124
42DAP/reference	0.98789	0.594
43DAP/reference	1.16111	0.845
47DAP/reference	0.91754	0.188
52DAP/reference	0.75883	0.086
57DAP/reference	0.95513	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.59196	0.025
17DAP/reference	2.38482	0.206
27DAP/reference	4.75544	0.016
39DAP/reference	5.44521	0.011
41DAP/reference	5.20167	0.009
42DAP/reference	5.52272	0.014
43DAP/reference	4.53652	0.022
47DAP/reference	0.8231	0.054
52DAP/reference	5.00589	0.052
57DAP/reference	2.32944	0.706

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.54267	0.631
26DAP/20DAP	2.43346	0.118
34DAP/26DAP	1.14989	1
51DAP/34DAP	1.01908	0.98
52DAP/51DAP	0.70615	1
53DAP/52DAP	1.0571	0.91
55DAP/53DAP	0.83236	0.144
57DAP/55DAP	1.11148	0.881
62DAP/57DAP	1.00547	1
68DAP/62DAP	0.98739	0.885
68DAP/14DAP	0.8348	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75881	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.239	0.113
Mature Green Tomato/Ripe Tomato	3.49204	0.015
Immature Eggplant/Mature Eggplant	0.88729	0.223
Ripe Pepper/Ripe Tomato	1.77041	1
Mature Eggplant/Ripe Tomato	1.51809	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16643	0.536
1-1-2/M82	1.28597	1
12-2/M82	1.01127
12-4/M82	1.00554	1
1-3/M82	N/A	N/A
2-1-1/M82	1.04532
2-1/M82	0.89061
2-6/M82	N/A	N/A
3-2/M82	1.13021	0.549
4-1-1/M82	1.01539	1
4-1/M82	N/A	N/A
4-3-2/M82	1.37263	0.508
4-3/M82	1.15183	1
5-3/M82	1.00178	1
6-2/M82	0.9016
6-3/M82	1.08914	1
7-1/M82	1.0353
7-2/M82	0.98787
9-3-2/M82	1.10479	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96679	1
IL2-6/WTpooled	0.96016	1
IL7-5/WTpooled	0.82921	1
IL7-3/WTpooled	1.00545	1
IL12-4/WTpooled	1.02836	0.891
IL1-4/WTpooled	0.91852	0.834
WT/WTpooled	1.02484	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	0.98454	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15871	0.846
DC3000/delta hrp 6h	1.08988	1
DC3000/delta hrp 12h	0.92956	1
DC3000/delta hrp 24h	1.12398	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79349	0.105
DC3000 delta B/DC3000 delta AB	0.7124	0.036

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93736	1
Exp 36h	0.66258	0.426
Exp 60h	0.59345	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00426	1
Var 0h	0.84409	0.933
Var 12h I row2-row1	0.7577	0.318
Var 12h NI row2-row1	1.02039	1
Var 36h I row2-row1	1.07786	1
Var 36h NI row2-row1	1.59107	1
Var 60h I row2-row1	1.30784	1
Var 60h NI row2-row1	1.03382	1
Time course 0hI-0hNI	0.9294	0.43
Time course 12hI-12hNI	0.84848	0.082
Time course 36hI-36hNI	0.62039	0.023
Time course 60hI-60hNI	0.20665	0.005

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)	0.89651	0.267
transgenic ySAMdc/azygous control (breaker)	0.72908	0.124
transgenic ySAMdc/azygous control (red)	0.9754	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06658	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.54986	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07516	0.307
Manapal/WT (break)	1.03058	1
Manapal/WT (red)	0.76606	0.181