Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19742	0.615
27DAP/17DAP	1.64893	0.686
39DAP/27DAP	1.01579	0.782
41DAP/39DAP	1.36298	0.511
42DAP/41DAP	1.28129	0.82
43DAP/42DAP	0.86766	0.807
47DAP/43DAP	0.93839	0.716
52DAP/47DAP	0.90833	0.705
57DAP/52DAP	1.27373	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96517	0.336
17DAP/reference	0.98219	0.503
27DAP/reference	0.95112	0.275
39DAP/reference	1.00365	0.828
41DAP/reference	1.00828	0.963
42DAP/reference	0.99886	0.665
43DAP/reference	1.01392	0.812
47DAP/reference	0.9638	0.161
52DAP/reference	0.92862	0.195
57DAP/reference	0.92872	0.074

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99187	0.801
27DAP/17DAP	0.97976	0.821
39DAP/27DAP	1.06067	0.471
41DAP/39DAP	1.01965	1
42DAP/41DAP	1.07418	0.559
43DAP/42DAP	0.97812	0.665
47DAP/43DAP	0.97502	0.823
52DAP/47DAP	1.04684	0.816
57DAP/52DAP	1.04193	0.722
57DAP/7DAP	1.08601	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96657	0.138
17DAP/reference	0.94473	0.025
27DAP/reference	0.91207	0.01
39DAP/reference	1.03186	0.166
41DAP/reference	1.0479	0.241
42DAP/reference	1.05541	0.076
43DAP/reference	1.00202	1
47DAP/reference	0.9543	0.293
52DAP/reference	1.01664	0.781
57DAP/reference	1.02443	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99159	0.848
17DAP/reference	0.9647	0.367
27DAP/reference	0.90283	0.16
39DAP/reference	0.9643	0.416
41DAP/reference	1.52755	0.459
42DAP/reference	0.87725	0.02
43DAP/reference	1.02811	0.704
47DAP/reference	0.914	0.09
52DAP/reference	0.91088	0.101
57DAP/reference	0.94299	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9236	0.049
17DAP/reference	0.96395	0.214
27DAP/reference	1.01165	0.777
39DAP/reference	1.0265	0.67
41DAP/reference	0.95821	0.293
42DAP/reference	0.81033	0.172
43DAP/reference	0.92941	0.084
47DAP/reference	0.96733	0.452
52DAP/reference	0.93404	0.228
57DAP/reference	0.7491	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87141	0.611
26DAP/20DAP	0.90295	0.512
34DAP/26DAP	0.89875	0.253
51DAP/34DAP	0.9972	0.946
52DAP/51DAP	1.0346	0.662
53DAP/52DAP	0.90385	0.572
55DAP/53DAP	1.06875	0.781
57DAP/55DAP	1.07829	0.955
62DAP/57DAP	0.86983	0.871
68DAP/62DAP	0.92063	0.722
68DAP/14DAP	1.29159	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97887	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48526	0.096
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.89049	0.407
Ripe Pepper/Ripe Tomato	1.49787	0.258
Mature Eggplant/Ripe Tomato	0.92901	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04501	1
1-1-2/M82	0.94582	0.804
12-2/M82	0.96649	0.955
12-4/M82	1.00465	1
1-3/M82	1.0449	1
2-1-1/M82	1.10467	0.764
2-1/M82	N/A	N/A
2-6/M82	0.89333	1
3-2/M82	1.03287
4-1-1/M82	1.14861	0.977
4-1/M82	0.9942
4-3-2/M82	0.9459
4-3/M82	0.903	1
5-3/M82	1.01004	1
6-2/M82	1.02645	1
6-3/M82	1.07221	1
7-1/M82	1.1355
7-2/M82	0.93581
9-3-2/M82	N/A	N/A

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	N/A	N/A
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	0.88383	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97984	1
DC3000/delta hrp 6h	1.11272	1
DC3000/delta hrp 12h	0.89544	1
DC3000/delta hrp 24h	0.98204	0.945

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0113	0.515
DC3000 delta B/DC3000 delta AB	0.98988	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04931	1
Exp 36h	0.95196	0.449
Exp 60h	0.78343	0.253

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	N/A	N/A
Var 12h I row2-row1	1.07728	0.201
Var 12h NI row2-row1	1.09337	1
Var 36h I row2-row1	0.83478
Var 36h NI row2-row1	0.7146
Var 60h I row2-row1	1.84918
Var 60h NI row2-row1	1.19278	0.904
Time course 0hI-0hNI	1.16095	0.262
Time course 12hI-12hNI	0.88761	0.6
Time course 36hI-36hNI	0.89879	0.084
Time course 60hI-60hNI	0.89536	0.646

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)	1.00406	1
transgenic ySAMdc/azygous control (breaker)	1.02489	1
transgenic ySAMdc/azygous control (red)	0.94623	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00368	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69734	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71483	0.172
Manapal/WT (break)	0.84978	1
Manapal/WT (red)	0.85969	0.184