Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03742	0.904
27DAP/17DAP	1.47277	0.927
39DAP/27DAP	1.44266	0.691
41DAP/39DAP	1.19552	0.814
42DAP/41DAP	1.71071	0.671
43DAP/42DAP	1.14698	0.937
47DAP/43DAP	1.52663	0.497
52DAP/47DAP	1.20316	0.715
57DAP/52DAP	0.74431	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85323	0.068
17DAP/reference	0.94915	0.368
27DAP/reference	0.82838	0.075
39DAP/reference	0.96973	0.691
41DAP/reference	0.91087	0.154
42DAP/reference	1.03413	1
43DAP/reference	1.18565	0.021
47DAP/reference	1.23062	0.001
52DAP/reference	1.22785	0.035
57DAP/reference	1.30442	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9715	0.697
27DAP/17DAP	1.16286	0.681
39DAP/27DAP	1.18795	0.275
41DAP/39DAP	0.98591	0.997
42DAP/41DAP	1.138	0.824
43DAP/42DAP	1.02936	1
47DAP/43DAP	1.09277	0.857
52DAP/47DAP	0.94832	0.839
57DAP/52DAP	1.10786	0.574
57DAP/7DAP	1.69514	0.207

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20368	0.193
17DAP/reference	0.91981	0.22
27DAP/reference	0.98184	0.53
39DAP/reference	0.91126	0.17
41DAP/reference	1.00513	1
42DAP/reference	0.86721	0.055
43DAP/reference	0.84642	0.1
47DAP/reference	0.99753	1
52DAP/reference	1.0459	0.636
57DAP/reference	0.86806	0.128

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82631	0.023
17DAP/reference	0.88961	0.077
27DAP/reference	0.8737	0.167
39DAP/reference	0.87265	0.062
41DAP/reference	0.86014	0.066
42DAP/reference	0.86575	0.081
43DAP/reference	0.86582	0.269
47DAP/reference	0.92275	0.113
52DAP/reference	0.75109	0.006
57DAP/reference	0.81713	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90953	0.249
17DAP/reference	0.85909	0.124
27DAP/reference	0.95506	0.337
39DAP/reference	0.829	0.022
41DAP/reference	0.95146	0.459
42DAP/reference	0.94307	0.445
43DAP/reference	1.21708	0.09
47DAP/reference	1.07211	0.704
52DAP/reference	1.02336	0.979
57DAP/reference	0.90126	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30155	0.966
26DAP/20DAP	1.37306	0.53
34DAP/26DAP	0.75741	0.127
51DAP/34DAP	0.86649	0.333
52DAP/51DAP	1.06938	0.349
53DAP/52DAP	0.96294	0.868
55DAP/53DAP	0.92599	0.725
57DAP/55DAP	1.16809	0.947
62DAP/57DAP	1.00882	1
68DAP/62DAP	1.19687	0.813
68DAP/14DAP	4.91831	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42282	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97503	0.805
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.93149	0.407
Ripe Pepper/Ripe Tomato	0.90441	1
Mature Eggplant/Ripe Tomato	1.51675	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08703
1-1-2/M82	1.0182	1
12-2/M82	N/A	N/A
12-4/M82	0.82059	0.619
1-3/M82	N/A	N/A
2-1-1/M82	1.11713
2-1/M82	N/A	N/A
2-6/M82	0.88162
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	1.41166
4-3/M82	2.08054	1
5-3/M82	0.8135	1
6-2/M82	N/A	N/A
6-3/M82	0.77011	0.68
7-1/M82	N/A	N/A
7-2/M82	1.19275
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97134	1
IL2-6/WTpooled	1.11899
IL7-5/WTpooled	0.95651	1
IL7-3/WTpooled	0.60204	0.293
IL12-4/WTpooled	1.25033	0.737
IL1-4/WTpooled	1.08632	1
WT/WTpooled	0.98312	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	0.81457	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.3391	0.914
DC3000/delta hrp 6h	1.00618
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.12513	0.383

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	1.34654	0.443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12212	1
Exp 36h	0.94983	0.879
Exp 60h	0.99911	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03903	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.92271	0.77
Var 12h NI row2-row1	1.13238	0.34
Var 36h I row2-row1	1.00133	1
Var 36h NI row2-row1	0.88834	0.61
Var 60h I row2-row1	0.83335	0.832
Var 60h NI row2-row1	0.89561	0.932
Time course 0hI-0hNI	0.94778	0.755
Time course 12hI-12hNI	1.07991	0.663
Time course 36hI-36hNI	0.94351	0.295
Time course 60hI-60hNI	1.24146	0.013

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)	1.07087	0.397
transgenic ySAMdc/azygous control (breaker)	0.77231	0.132
transgenic ySAMdc/azygous control (red)	0.92778	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10414	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7243	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83571	1
Manapal/WT (break)	0.86702	0.333
Manapal/WT (red)	0.97359	0.863