Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.1.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.57265	0.281
27DAP/17DAP	1.3561	0.632
39DAP/27DAP	1.27176	0.473
41DAP/39DAP	0.52484	0.041
42DAP/41DAP	2.56702	0.021
43DAP/42DAP	1.96229	0.402
47DAP/43DAP	2.08367	0.213
52DAP/47DAP	1.55484	0.359
57DAP/52DAP	1.83382	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1934	0.015
17DAP/reference	1.16601	0.019
27DAP/reference	1.21135	0.025
39DAP/reference	1.1175	0.218
41DAP/reference	1.14865	0.034
42DAP/reference	1.17182	0.009
43DAP/reference	1.04414	0.928
47DAP/reference	1.17239	0.004
52DAP/reference	1.14994	0.045
57DAP/reference	1.03489	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27279	0.111
27DAP/17DAP	1.11303	0.775
39DAP/27DAP	1.01015	1
41DAP/39DAP	1.35791	1
42DAP/41DAP	1.80762	0.042
43DAP/42DAP	1.33521	0.192
47DAP/43DAP	1.15713	0.448
52DAP/47DAP	1.79675	0.1
57DAP/52DAP	1.26196	0.335
57DAP/7DAP	3.73682	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93337	0.27
17DAP/reference	0.89232	0.082
27DAP/reference	0.93347	0.264
39DAP/reference	0.88137	0.083
41DAP/reference	1.10094	0.375
42DAP/reference	1.0443	0.686
43DAP/reference	1.01772	0.802
47DAP/reference	1.11615	0.235
52DAP/reference	1.00971	1
57DAP/reference	0.96045	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22298	0.108
17DAP/reference	1.29848	0.011
27DAP/reference	1.35164	0.026
39DAP/reference	1.44014	0.046
41DAP/reference	1.40121	0.009
42DAP/reference	1.11023	0.466
43DAP/reference	1.12531	0.497
47DAP/reference	1.17674	0.022
52DAP/reference	1.30543	0.013
57DAP/reference	1.47459	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97673	0.566
17DAP/reference	0.90734	0.286
27DAP/reference	0.89965	0.206
39DAP/reference	0.93719	0.271
41DAP/reference	0.90514	0.167
42DAP/reference	1.12559	0.307
43DAP/reference	1.05433	0.755
47DAP/reference	1.25616	0.06
52DAP/reference	0.89127	0.334
57DAP/reference	1.22189	0.255

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0352	1
26DAP/20DAP	0.98457	1
34DAP/26DAP	1.43083	1
51DAP/34DAP	3.07491	0.033
52DAP/51DAP	0.99709	1
53DAP/52DAP	1.06046	0.944
55DAP/53DAP	0.8313	0.325
57DAP/55DAP	1.06773	0.805
62DAP/57DAP	0.88252	0.681
68DAP/62DAP	0.78849	0.668
68DAP/14DAP	0.77586	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	19.9443	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2451	0.068
Mature Green Tomato/Ripe Tomato	0.16876	0.017
Immature Eggplant/Mature Eggplant	1.10136	0.205
Ripe Pepper/Ripe Tomato	0.45692	1
Mature Eggplant/Ripe Tomato	0.49608	1

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	1.19841
1-3/M82	1.48397
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	1.03404	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.83168
4-3/M82	N/A	N/A
5-3/M82	2.37874	0.447
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.21417
7-2/M82	1.03739
9-3-2/M82	2.16532	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.67421	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.8519	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.97429	1
IL1-4/WTpooled	0.82146	0.415
WT/WTpooled	1.03651

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	1.0242	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93037	1
DC3000/delta hrp 6h	0.93061	0.95
DC3000/delta hrp 12h	1.25677	1
DC3000/delta hrp 24h	0.80291	0.05

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	0.87605

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08511	1
Var 0h	0.77633	0.594
Var 12h I row2-row1	0.86182	0.338
Var 12h NI row2-row1	0.78316	0.713
Var 36h I row2-row1	0.89863	0.805
Var 36h NI row2-row1	0.81429	1
Var 60h I row2-row1	1.19168	1
Var 60h NI row2-row1	1.05353	0.904
Time course 0hI-0hNI	1.08163	0.63
Time course 12hI-12hNI	0.87	0.246
Time course 36hI-36hNI	0.81608	0.058
Time course 60hI-60hNI	0.63242	0.009

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)	1.14632	0.654
transgenic ySAMdc/azygous control (breaker)	0.5481	0.15
transgenic ySAMdc/azygous control (red)	1.24379	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1786	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17319	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86552	1
Manapal/WT (break)	0.57431	1
Manapal/WT (red)	0.68445	0.424