Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.14.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00052	0.847
27DAP/17DAP	0.91581	0.833
39DAP/27DAP	1.03879	0.995
41DAP/39DAP	1.27858	0.334
42DAP/41DAP	1.02772	1
43DAP/42DAP	1.06445	1
47DAP/43DAP	1.1126	0.825
52DAP/47DAP	0.82472	0.515
57DAP/52DAP	0.96256	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09235	0.421
17DAP/reference	0.95886	0.321
27DAP/reference	0.98435	0.694
39DAP/reference	0.91002	0.24
41DAP/reference	0.9416	0.434
42DAP/reference	0.89514	0.013
43DAP/reference	1.01615	0.838
47DAP/reference	0.97103	0.3
52DAP/reference	0.87072	0.064
57DAP/reference	0.9408	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01125	0.923
27DAP/17DAP	1.00131	1
39DAP/27DAP	1.0057	1
41DAP/39DAP	1.07751	0.69
42DAP/41DAP	1.0195	0.927
43DAP/42DAP	1.08929	0.192
47DAP/43DAP	1.04307	0.822
52DAP/47DAP	1.02704	0.919
57DAP/52DAP	1.02958	0.856
57DAP/7DAP	1.00891	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56009	0.062
17DAP/reference	0.37635	0.011
27DAP/reference	0.38851	0.01
39DAP/reference	0.30523	0.011
41DAP/reference	0.75034	0.09
42DAP/reference	0.26719	0.01
43DAP/reference	0.28103	0.008
47DAP/reference	0.71142	0.222
52DAP/reference	0.23901	0.009
57DAP/reference	0.22434	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90047	0.041
17DAP/reference	0.95182	0.279
27DAP/reference	0.95973	0.438
39DAP/reference	0.86275	0.173
41DAP/reference	0.99461	0.505
42DAP/reference	0.93834	0.433
43DAP/reference	0.70964	0.092
47DAP/reference	0.86586	0.045
52DAP/reference	0.88604	0.012
57DAP/reference	0.95591	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68163	0.119
17DAP/reference	0.9099	0.268
27DAP/reference	0.38466	0.03
39DAP/reference	0.41552	0.012
41DAP/reference	0.57528	0.086
42DAP/reference	0.39046	0.018
43DAP/reference	0.42805	0.024
47DAP/reference	0.94171	0.207
52DAP/reference	0.63293	0.131
57DAP/reference	0.86198	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05904	0.966
26DAP/20DAP	1.04121	0.886
34DAP/26DAP	1.09616	0.819
51DAP/34DAP	1.14011	0.458
52DAP/51DAP	1.00152	1
53DAP/52DAP	1.01699	0.91
55DAP/53DAP	1.04292	0.719
57DAP/55DAP	0.92512	0.638
62DAP/57DAP	0.92629	0.681
68DAP/62DAP	1.12591	0.808
68DAP/14DAP	1.21291	0.047

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85131	0.048

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91566	0.491
Mature Green Tomato/Ripe Tomato	0.99504	0.835
Immature Eggplant/Mature Eggplant	1.08238	0.239
Ripe Pepper/Ripe Tomato	2.18283	1
Mature Eggplant/Ripe Tomato	1.57694	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0203
1-1-2/M82	0.88027
12-2/M82	N/A	N/A
12-4/M82	0.81015	0.619
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	1.00135
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.9131
4-3-2/M82	1.23835
4-3/M82	1.61004
5-3/M82	1.09826	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.12951	0.741
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	1.86084	0.277
IL2-6/WTpooled	0.59474	0.358
IL7-5/WTpooled	1.09813	0.792
IL7-3/WTpooled	1.34756	1
IL12-4/WTpooled	1.2086	0.516
IL1-4/WTpooled	0.96554	1
WT/WTpooled	0.96593	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	1.1081	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11764	0.823
DC3000/delta hrp 6h	0.95071	0.95
DC3000/delta hrp 12h	0.91997	1
DC3000/delta hrp 24h	0.93525	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03515	0.515
DC3000 delta B/DC3000 delta AB	0.93207	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96912	1
Exp 36h	1.00588	1
Exp 60h	0.87532	0.386

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	1.55613
Var 12h I row2-row1	1.05805
Var 12h NI row2-row1	0.88553
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.77761
Var 60h NI row2-row1	0.90814	0.977
Time course 0hI-0hNI	0.91234
Time course 12hI-12hNI	1.00711	1
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.05242	0.482
transgenic ySAMdc/azygous control (breaker)	0.84099	0.251
transgenic ySAMdc/azygous control (red)	0.87984	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87071	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.80527	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10816	0.307
Manapal/WT (break)	1.35262	0.13
Manapal/WT (red)	1.44221	0.413