Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90384	0.253
27DAP/17DAP	0.82743	0.626
39DAP/27DAP	0.88747	0.583
41DAP/39DAP	0.69493	0.183
42DAP/41DAP	1.57156	0.767
43DAP/42DAP	0.82905	0.736
47DAP/43DAP	1.06983	0.965
52DAP/47DAP	1.28936	0.61
57DAP/52DAP	1.11036	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0344	0.735
17DAP/reference	0.93905	0.26
27DAP/reference	0.88574	0.089
39DAP/reference	1.009	0.903
41DAP/reference	0.92938	0.267
42DAP/reference	1.09154	0.144
43DAP/reference	0.99113	0.82
47DAP/reference	1.06646	0.136
52DAP/reference	1.17689	0.027
57DAP/reference	1.07413	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97903	0.763
27DAP/17DAP	1.22157	0.598
39DAP/27DAP	1.13519	0.514
41DAP/39DAP	1.02241	1
42DAP/41DAP	0.99746	0.887
43DAP/42DAP	1.05039	0.788
47DAP/43DAP	1.09253	0.822
52DAP/47DAP	1.12051	0.799
57DAP/52DAP	0.77189	0.206
57DAP/7DAP	1.0822

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26847	0.124
17DAP/reference	1.11086	0.269
27DAP/reference	1.09572	0.453
39DAP/reference	1.65819	0.007
41DAP/reference	1.74526	0.009
42DAP/reference	1.34849	0.233
43DAP/reference	1.55202	0.013
47DAP/reference	1.22669	0.182
52DAP/reference	1.64887	0.011
57DAP/reference	1.67453	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9992	0.93
17DAP/reference	1.234	0.079
27DAP/reference	1.10555	0.419
39DAP/reference	1.09713	0.489
41DAP/reference	1.12634	0.209
42DAP/reference	1.09566	0.455
43DAP/reference	0.98993	0.706
47DAP/reference	1.16856	0.089
52DAP/reference	1.00323	1
57DAP/reference	0.99112	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15762	0.827
17DAP/reference	0.9543	0.508
27DAP/reference	1.08182	0.179
39DAP/reference	1.24387	0.022
41DAP/reference	1.24181	0.115
42DAP/reference	1.15869	0.239
43DAP/reference	0.94308	0.319
47DAP/reference	1.10472	0.147
52DAP/reference	1.4563	0.079
57DAP/reference	1.48564	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.42193	0.631
26DAP/20DAP	0.91961
34DAP/26DAP	1.29183	1
51DAP/34DAP	2.1985	0.092
52DAP/51DAP	1.02193	1
53DAP/52DAP	1.26083	0.502
55DAP/53DAP	1.00137	0.951
57DAP/55DAP	0.90352	0.644
62DAP/57DAP	1.91343	0.002
68DAP/62DAP	0.99447	0.885
68DAP/14DAP	0.79024	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05388	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.47806	0.058
Mature Green Tomato/Ripe Tomato	1.46233	0.036
Immature Eggplant/Mature Eggplant	0.84108	0.176
Ripe Pepper/Ripe Tomato	0.78783	1
Mature Eggplant/Ripe Tomato	0.91367	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.72804
1-1-2/M82	1.02447	0.972
12-2/M82	N/A	N/A
12-4/M82	0.8207	0.358
1-3/M82	N/A	N/A
2-1-1/M82	1.05464
2-1/M82	N/A	N/A
2-6/M82	0.89587	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.54898
4-3-2/M82	N/A	N/A
4-3/M82	0.8321
5-3/M82	1.05457	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.85381
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.57289	0.277
IL2-6/WTpooled	0.40949	0.383
IL7-5/WTpooled	0.33794
IL7-3/WTpooled	1.72149	1
IL12-4/WTpooled	0.93112	0.566
IL1-4/WTpooled	1.12226	0.426
WT/WTpooled	0.93401	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	0.92718	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0675	0.921
DC3000/delta hrp 6h	0.94212	0.95
DC3000/delta hrp 12h	0.98281	1
DC3000/delta hrp 24h	0.97446	0.851

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	0.84745	1
Exp 36h	1.19707	0.693
Exp 60h	1.07969	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96884	1
Var 0h	1.30371	0.594
Var 12h I row2-row1	1.16938	0.235
Var 12h NI row2-row1	1.02363
Var 36h I row2-row1	0.91177	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.552	0.69
Time course 0hI-0hNI	0.85195	0.241
Time course 12hI-12hNI	1.01448	0.818
Time course 36hI-36hNI	0.94404	0.352
Time course 60hI-60hNI	0.89486	0.081

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)	1.03488	0.511
transgenic ySAMdc/azygous control (breaker)	1.3779	1
transgenic ySAMdc/azygous control (red)	1.1788	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98156	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86198	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95836	1
Manapal/WT (break)	1.13256	0.14
Manapal/WT (red)	1.25473	0.133