Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.4.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91057	0.532
27DAP/17DAP	1.14657	0.9
39DAP/27DAP	1.45861	0.198
41DAP/39DAP	0.85075	0.436
42DAP/41DAP	1.05383	0.994
43DAP/42DAP	0.98768	0.934
47DAP/43DAP	0.86275	0.562
52DAP/47DAP	1.30688	0.791
57DAP/52DAP	1.35484	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12381	0.366
17DAP/reference	1.14379	0.185
27DAP/reference	1.35077	0.039
39DAP/reference	1.46812	0.024
41DAP/reference	1.38409	0.023
42DAP/reference	1.37643	0.001
43DAP/reference	1.28134	0.02
47DAP/reference	1.64703	0.001
52DAP/reference	1.62975	0.018
57DAP/reference	1.82399	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88495	0.299
27DAP/17DAP	0.93271	0.782
39DAP/27DAP	0.84403	0.279
41DAP/39DAP	1.10526	0.79
42DAP/41DAP	1.21449	0.014
43DAP/42DAP	0.81419	0.054
47DAP/43DAP	0.85438	0.141
52DAP/47DAP	2.52197	0.044
57DAP/52DAP	2.61596	0.039
57DAP/7DAP	1.42503	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20581	0.147
17DAP/reference	1.2156	0.009
27DAP/reference	1.20954	0.018
39DAP/reference	1.37991	0.006
41DAP/reference	1.16281	0.064
42DAP/reference	1.30137	0.011
43DAP/reference	1.06702	0.289
47DAP/reference	1.25611	0.048
52DAP/reference	1.26719	0.012
57DAP/reference	1.27332	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09415	0.384
17DAP/reference	1.29995	0.023
27DAP/reference	1.47934	0.02
39DAP/reference	1.54282	0.016
41DAP/reference	1.16898	0.194
42DAP/reference	1.43298	0.011
43DAP/reference	1.05379	1
47DAP/reference	1.4239	0.024
52DAP/reference	0.84349	0.121
57DAP/reference	0.95796	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25711	0.041
17DAP/reference	0.95935	0.358
27DAP/reference	1.14167	0.164
39DAP/reference	1.13709	0.12
41DAP/reference	1.10557	0.112
42DAP/reference	1.22298	0.154
43DAP/reference	1.34174	0.25
47DAP/reference	0.96326	0.494
52DAP/reference	1.14718	0.335
57DAP/reference	2.30971	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.41015	0.966
26DAP/20DAP	1.40998	1
34DAP/26DAP	2.21394	0.819
51DAP/34DAP	1.56352	0.883
52DAP/51DAP	3.90212	0.035
53DAP/52DAP	0.65448	0.049
55DAP/53DAP	1.68703	0.039
57DAP/55DAP	0.63878	0.106
62DAP/57DAP	2.78254
68DAP/62DAP	0.69204	0.609
68DAP/14DAP	0.88888

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.32968	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87739	0.377
Mature Green Tomato/Ripe Tomato	2.49847	0.053
Immature Eggplant/Mature Eggplant	1.12868	0.3
Ripe Pepper/Ripe Tomato	1.42125	1
Mature Eggplant/Ripe Tomato	1.60214	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95969	0.944
1-1-2/M82	1.17183	0.977
12-2/M82	0.84225	0.955
12-4/M82	0.96773	1
1-3/M82	1.57522
2-1-1/M82	0.8827	0.92
2-1/M82	0.59951	0.322
2-6/M82	0.83928	0.501
3-2/M82	1.4334
4-1-1/M82	1.4881	0.876
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.28229	1
5-3/M82	1.18676	0.496
6-2/M82	N/A	N/A
6-3/M82	0.66879	0.916
7-1/M82	0.87905	0.476
7-2/M82	1.20677	1
9-3-2/M82	1.17113

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89631	1
IL2-6/WTpooled	1.06691	0.788
IL7-5/WTpooled	2.07223
IL7-3/WTpooled	1.1728	1
IL12-4/WTpooled	0.9409	1
IL1-4/WTpooled	0.82144	0.699
WT/WTpooled	1.13144	0.692

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	0.9786	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11244	0.715
DC3000/delta hrp 6h	0.84725	0.95
DC3000/delta hrp 12h	0.96665	1
DC3000/delta hrp 24h	0.9248	0.379

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22836	0.068
DC3000 delta B/DC3000 delta AB	1.47975	0.097

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04576	1
Exp 36h	1.05237	1
Exp 60h	0.98582	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.99657	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.9656	0.428
transgenic ySAMdc/azygous control (breaker)	0.77893	0.251
transgenic ySAMdc/azygous control (red)	0.99255	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18809	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96552	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77969	0.172
Manapal/WT (break)	1.1904	0.183
Manapal/WT (red)	1.8508	0.133