Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.14.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78955	0.217
27DAP/17DAP	1.41367	0.688
39DAP/27DAP	1.1064	0.853
41DAP/39DAP	1.50566	0.535
42DAP/41DAP	1.11477	0.876
43DAP/42DAP	1.00457	0.937
47DAP/43DAP	0.97115	0.828
52DAP/47DAP	0.84343	0.595
57DAP/52DAP	0.96479	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84249	0.071
17DAP/reference	0.96875	0.597
27DAP/reference	0.93466	0.395
39DAP/reference	0.97355	0.638
41DAP/reference	0.88929	0.341
42DAP/reference	0.78168	0.009
43DAP/reference	0.91253	0.448
47DAP/reference	0.83545	0.023
52DAP/reference	0.87289	0.158
57DAP/reference	1.01679	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83592	0.311
27DAP/17DAP	1.20272	0.194
39DAP/27DAP	1.22479	0.672
41DAP/39DAP	0.78535	0.09
42DAP/41DAP	1.28013	0.727
43DAP/42DAP	1.07065	0.627
47DAP/43DAP	1.12378	0.5
52DAP/47DAP	0.88711	0.472
57DAP/52DAP	0.92912	0.603
57DAP/7DAP	1.08153	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9229	0.27
17DAP/reference	1.00436	0.693
27DAP/reference	1.08708	0.804
39DAP/reference	0.85039	0.095
41DAP/reference	1.1793	0.43
42DAP/reference	1.05849	0.828
43DAP/reference	1.10007	1
47DAP/reference	0.90062	0.504
52DAP/reference	0.77112	0.035
57DAP/reference	0.95809	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04473	0.943
17DAP/reference	0.96218	0.51
27DAP/reference	1.03936	1
39DAP/reference	0.76188	0.074
41DAP/reference	0.72634	0.053
42DAP/reference	0.77665	0.037
43DAP/reference	0.91782	0.285
47DAP/reference	0.88599	0.214
52DAP/reference	0.84848	0.066
57DAP/reference	1.01252	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03474	0.804
17DAP/reference	0.93351	0.488
27DAP/reference	1.03621	0.552
39DAP/reference	1.0994	0.65
41DAP/reference	0.92706	0.264
42DAP/reference	0.86059	0.172
43DAP/reference	0.72485	0.028
47DAP/reference	0.8096	0.019
52DAP/reference	1.40736	0.876
57DAP/reference	0.96011	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.50091	0.966
26DAP/20DAP	1.06809	0.886
34DAP/26DAP	1.06677	1
51DAP/34DAP	1.06246	0.993
52DAP/51DAP	0.84585	1
53DAP/52DAP	1.10575	0.552
55DAP/53DAP	1.1425	0.241
57DAP/55DAP	1.23077	0.818
62DAP/57DAP	1.37005	0.8
68DAP/62DAP	0.98579	0.769
68DAP/14DAP	1.33413	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08565	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79909	0.309
Mature Green Tomato/Ripe Tomato	0.27374	0.018
Immature Eggplant/Mature Eggplant	2.43423	0.05
Ripe Pepper/Ripe Tomato	1.74446
Mature Eggplant/Ripe Tomato	1.24239	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19134
1-1-2/M82	0.99065
12-2/M82	N/A	N/A
12-4/M82	0.88432
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	1.03381
5-3/M82	0.73691	0.447
6-2/M82	N/A	N/A
6-3/M82	1.17723
7-1/M82	N/A	N/A
7-2/M82	1.07914
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88232	0.247
IL2-6/WTpooled	0.63333	0.473
IL7-5/WTpooled	0.98092	1
IL7-3/WTpooled	1.59103	1
IL12-4/WTpooled	1.01918	1
IL1-4/WTpooled	1.0753	1
WT/WTpooled	1.03487	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	0.91694	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04383	0.921
DC3000/delta hrp 6h	0.91728	0.95
DC3000/delta hrp 12h	0.91423	1
DC3000/delta hrp 24h	1.15703	0.088

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85111	0.485
DC3000 delta B/DC3000 delta AB	0.82302	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.62762	1
Exp 60h	1.37328	1

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	0.5486	0.936
Var 12h I row2-row1	1.16485	0.196
Var 12h NI row2-row1	1.00466	1
Var 36h I row2-row1	0.79901	1
Var 36h NI row2-row1	0.96331	0.791
Var 60h I row2-row1	0.87195	0.285
Var 60h NI row2-row1	1.14258	0.904
Time course 0hI-0hNI	1.02639	0.852
Time course 12hI-12hNI	1.20614	0.093
Time course 36hI-36hNI	1.16184	0.128
Time course 60hI-60hNI	1.20711	0.069

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)	1.01865	0.541
transgenic ySAMdc/azygous control (breaker)	1.28591	0.172
transgenic ySAMdc/azygous control (red)	0.8573	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28718	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10379	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05601	0.096
Manapal/WT (break)	1.05579	1
Manapal/WT (red)	0.65436	0.181