Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.14.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87138	0.413
27DAP/17DAP	0.75054	0.403
39DAP/27DAP	0.85585	0.549
41DAP/39DAP	0.92393	0.717
42DAP/41DAP	0.84759	0.774
43DAP/42DAP	1.09542	1
47DAP/43DAP	0.94705	0.788
52DAP/47DAP	1.06509	0.915
57DAP/52DAP	1.29947	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93576	0.371
17DAP/reference	0.8171	0.035
27DAP/reference	1.1705	0.314
39DAP/reference	0.93375	0.455
41DAP/reference	0.72983	0.039
42DAP/reference	0.95704	0.259
43DAP/reference	1.22602	0.012
47DAP/reference	1.44746	0.048
52DAP/reference	1.52783	0.011
57DAP/reference	1.91309	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92994	0.509
27DAP/17DAP	1.01924	1
39DAP/27DAP	1.2848	0.253
41DAP/39DAP	1.03561	0.88
42DAP/41DAP	0.93527	0.595
43DAP/42DAP	0.93373	0.431
47DAP/43DAP	0.96718	0.833
52DAP/47DAP	1.72639	0.062
57DAP/52DAP	1.60769	0.168
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41663	0.163
17DAP/reference	2.55604
27DAP/reference	1.80156	0.041
39DAP/reference	N/A	N/A
41DAP/reference	1.78855	0.009
42DAP/reference	2.27842	0.076
43DAP/reference	2.53669	0.018
47DAP/reference	2.11863	0.028
52DAP/reference	2.02364	0.038
57DAP/reference	2.29782	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6614	0.006
17DAP/reference	0.54205	0.004
27DAP/reference	0.95393	0.467
39DAP/reference	1.13599	0.109
41DAP/reference	1.4625	0.007
42DAP/reference	1.27328	0.035
43DAP/reference	0.64865	0.135
47DAP/reference	1.20531	0.018
52DAP/reference	0.96418	0.302
57DAP/reference	0.77184	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15825	0.723
17DAP/reference	1.14567	0.81
27DAP/reference	3.30959	0.067
39DAP/reference	2.60214	0.116
41DAP/reference	2.43764	0.065
42DAP/reference	2.30507	0.008
43DAP/reference	1.70892	0.043
47DAP/reference	1.14957	0.792
52DAP/reference	2.26915	0.058
57DAP/reference	2.39316	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17439	0.678
26DAP/20DAP	3.0257	0.16
34DAP/26DAP	1.10236	1
51DAP/34DAP	1.09777	0.978
52DAP/51DAP	1.18997	0.606
53DAP/52DAP	0.90998	0.741
55DAP/53DAP	1.00959	1
57DAP/55DAP	0.40521	0.037
62DAP/57DAP	1.44587	0.158
68DAP/62DAP	5.19771	0.017
68DAP/14DAP	4.23751	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.50614

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23186	0.075
Mature Green Tomato/Ripe Tomato	1.12188	0.774
Immature Eggplant/Mature Eggplant	0.91532	0.197
Ripe Pepper/Ripe Tomato	2.06279	0.258
Mature Eggplant/Ripe Tomato	4.44321	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8594
1-1-2/M82	0.96542
12-2/M82	N/A	N/A
12-4/M82	0.90454	0.33
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	1.09627	0.572
6-2/M82	0.71931
6-3/M82	0.7892
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	0.82937	0.321
IL2-6/WTpooled	1.40697	0.409
IL7-5/WTpooled	1.32885	1
IL7-3/WTpooled	0.94731	1
IL12-4/WTpooled	1.07587	0.516
IL1-4/WTpooled	1.02126	1
WT/WTpooled	1.00438	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	0.97048	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95116	1
DC3000/delta hrp 6h	0.99551	0.95
DC3000/delta hrp 12h	0.85627	1
DC3000/delta hrp 24h	0.92432	0.483

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	0.94842	1
Exp 36h	1.01619	1
Exp 60h	0.97653	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03098	1
Var 0h	0.67598	1
Var 12h I row2-row1	0.59908	0.418
Var 12h NI row2-row1	1.246	0.34
Var 36h I row2-row1	1.10173	1
Var 36h NI row2-row1	2.66005	1
Var 60h I row2-row1	0.57348	0.306
Var 60h NI row2-row1	0.79514	0.756
Time course 0hI-0hNI	0.8901	0.452
Time course 12hI-12hNI	1.27796	0.327
Time course 36hI-36hNI	1.00769	0.468
Time course 60hI-60hNI	22.5338	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)	1.07428	0.287
transgenic ySAMdc/azygous control (breaker)	0.9149	0.49
transgenic ySAMdc/azygous control (red)	0.89377	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99127	0.588

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82921	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78264	1
Manapal/WT (break)	1.19851	0.14
Manapal/WT (red)	1.14219	0.222