Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.18.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95388	0.586
27DAP/17DAP	1.0837	0.849
39DAP/27DAP	1.23368	0.631
41DAP/39DAP	1.07283	0.904
42DAP/41DAP	1.04043	1
43DAP/42DAP	0.90715	0.827
47DAP/43DAP	0.68611	0.173
52DAP/47DAP	1.0023	0.982
57DAP/52DAP	1.29083	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06591	0.544
17DAP/reference	0.60184	0.008
27DAP/reference	0.77392	0.012
39DAP/reference	0.69101	0.014
41DAP/reference	0.68077	0.016
42DAP/reference	0.74638	0.001
43DAP/reference	0.79114	0.032
47DAP/reference	0.7492	0.001
52DAP/reference	0.78559	0.027
57DAP/reference	0.79279	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61746	0.116
27DAP/17DAP	1.04819	0.893
39DAP/27DAP	1.1315	0.677
41DAP/39DAP	0.85932	0.512
42DAP/41DAP	1.42541	0.005
43DAP/42DAP	1.16651	0.351
47DAP/43DAP	1.12711	0.206
52DAP/47DAP	0.74448	0.075
57DAP/52DAP	0.98308	0.789
57DAP/7DAP	0.55068	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26073	0.036
17DAP/reference	0.73905	0.02
27DAP/reference	0.7662	0.011
39DAP/reference	0.67619	0.011
41DAP/reference	0.87351	0.035
42DAP/reference	0.78382	0.033
43DAP/reference	0.85875	0.105
47DAP/reference	1.00307	1
52DAP/reference	0.83249	0.053
57DAP/reference	0.72429	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26776	0.626
17DAP/reference	0.50667	0.003
27DAP/reference	0.66402	0.013
39DAP/reference	0.61259	0.008
41DAP/reference	0.83876	0.11
42DAP/reference	0.80989	0.121
43DAP/reference	0.56563	0.002
47DAP/reference	0.69581	0.012
52DAP/reference	0.61714	0.004
57DAP/reference	0.52164	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28855	0.273
17DAP/reference	0.5889	0.007
27DAP/reference	0.60017	0.032
39DAP/reference	0.86993	0.043
41DAP/reference	0.83262	0.019
42DAP/reference	0.7732	0.028
43DAP/reference	0.855	0.116
47DAP/reference	0.74362	0.028
52DAP/reference	0.74368	0.137
57DAP/reference	0.81783	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14313	0.966
26DAP/20DAP	1.16228	0.727
34DAP/26DAP	1.058	1
51DAP/34DAP	2.2184	0.032
52DAP/51DAP	0.78397	0.151
53DAP/52DAP	1.939	0.027
55DAP/53DAP	1.03396	1
57DAP/55DAP	1.06673	0.855
62DAP/57DAP	0.86573	0.681
68DAP/62DAP	1.36688	0.247
68DAP/14DAP	3.54174	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6728	0.039

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.39362	0.082
Mature Green Tomato/Ripe Tomato	1.60058	0.209
Immature Eggplant/Mature Eggplant	1.93736	0.05
Ripe Pepper/Ripe Tomato	1.88518	0.258
Mature Eggplant/Ripe Tomato	1.46049	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10613	0.551
1-1-2/M82	0.86133	0.958
12-2/M82	0.86627	0.955
12-4/M82	0.80283	0.358
1-3/M82	1.38482	0.479
2-1-1/M82	1.09225	0.764
2-1/M82	1.21453	1
2-6/M82	1.08577	0.594
3-2/M82	1.4213
4-1-1/M82	0.96	1
4-1/M82	1.03327	1
4-3-2/M82	0.8093	0.487
4-3/M82	1.20243	0.268
5-3/M82	1.2871	0.496
6-2/M82	1.0126	1
6-3/M82	0.7772
7-1/M82	0.88564	1
7-2/M82	1.37429	0.324
9-3-2/M82	1.33161	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.67937
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.42634	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04748	0.921
DC3000/delta hrp 6h	0.90946	0.95
DC3000/delta hrp 12h	1.13278	1
DC3000/delta hrp 24h	2.98017	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.15085	0.102
DC3000 delta B/DC3000 delta AB	1.55908	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.51462	0.227
Exp 36h	3.25498	0.489
Exp 60h	2.30059	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01441	1
Var 0h	1.11825	0.936
Var 12h I row2-row1	1.58327	0.443
Var 12h NI row2-row1	4.36099	1
Var 36h I row2-row1	1.20331	0.908
Var 36h NI row2-row1	2.20343	1
Var 60h I row2-row1	0.83782	0.306
Var 60h NI row2-row1	0.72659	0.818
Time course 0hI-0hNI	1.12168	0.377
Time course 12hI-12hNI	1.29653	0.08
Time course 36hI-36hNI	3.09332	0.006
Time course 60hI-60hNI	19.0751	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)	1.16712	0.408
transgenic ySAMdc/azygous control (breaker)	1.45779	0.172
transgenic ySAMdc/azygous control (red)	0.89622	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.90691	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66923	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.37145	0.088
Manapal/WT (break)	0.92662	1
Manapal/WT (red)	0.54903	0.181