Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.16.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00634	0.975
27DAP/17DAP	1.12319	0.854
39DAP/27DAP	1.29014	0.493
41DAP/39DAP	1.01687	0.949
42DAP/41DAP	0.99287	1
43DAP/42DAP	0.88207	0.67
47DAP/43DAP	0.86724	0.58
52DAP/47DAP	1.4525	0.307
57DAP/52DAP	1.02146	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89253	0.078
17DAP/reference	0.90207	0.138
27DAP/reference	1.14689	0.291
39DAP/reference	0.99204	0.874
41DAP/reference	0.81946	0.154
42DAP/reference	0.89992	0.025
43DAP/reference	0.9231	0.17
47DAP/reference	1.13587	0.478
52DAP/reference	1.82341	0.02
57DAP/reference	1.29599	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98282	0.75
27DAP/17DAP	1.36817	0.271
39DAP/27DAP	0.96713	0.775
41DAP/39DAP	1.18957	0.565
42DAP/41DAP	0.94263	0.565
43DAP/42DAP	0.91011	0.206
47DAP/43DAP	1.0302	0.926
52DAP/47DAP	1.02698	0.975
57DAP/52DAP	1.11443	1
57DAP/7DAP	1.23504	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16564	0.298
17DAP/reference	0.94591	0.22
27DAP/reference	1.08485	0.131
39DAP/reference	1.17669	0.12
41DAP/reference	1.24218	0.069
42DAP/reference	1.25652	0.024
43DAP/reference	1.37836	0.028
47DAP/reference	1.52408	0.13
52DAP/reference	1.4893	0.013
57DAP/reference	1.36376	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79875	0.009
17DAP/reference	0.74101	0.005
27DAP/reference	0.93231	0.282
39DAP/reference	0.98678	0.569
41DAP/reference	0.94547	0.299
42DAP/reference	1.07929	0.794
43DAP/reference	0.77655	0.018
47DAP/reference	0.93236	0.284
52DAP/reference	0.87824	0.131
57DAP/reference	0.73169	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14658	0.224
17DAP/reference	0.91777	0.313
27DAP/reference	0.92906	0.081
39DAP/reference	1.25173	0.024
41DAP/reference	1.0174	1
42DAP/reference	1.03093	0.863
43DAP/reference	1.13431	0.439
47DAP/reference	0.94471	0.335
52DAP/reference	1.21119	0.233
57DAP/reference	1.61324	0.075

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12859	0.966
26DAP/20DAP	1.33436	0.442
34DAP/26DAP	0.92689	0.753
51DAP/34DAP	3.20688	0.021
52DAP/51DAP	0.77453	0.151
53DAP/52DAP	1.51018	0.027
55DAP/53DAP	1.20389	1
57DAP/55DAP	0.99446	0.795
62DAP/57DAP	1.11421	0.8
68DAP/62DAP	1.28367	0.413
68DAP/14DAP	3.64861	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59336	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52773	0.121
Mature Green Tomato/Ripe Tomato	0.64781	0.079
Immature Eggplant/Mature Eggplant	1.23458	0.13
Ripe Pepper/Ripe Tomato	1.0677	1
Mature Eggplant/Ripe Tomato	1.07197	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9831	0.961
1-1-2/M82	1.18232	1
12-2/M82	0.94873	0.955
12-4/M82	0.90848	1
1-3/M82	1.65374
2-1-1/M82	0.9077
2-1/M82	1.11407	1
2-6/M82	0.93157	1
3-2/M82	1.10365	0.461
4-1-1/M82	0.86517	1
4-1/M82	1.56149	0.466
4-3-2/M82	0.84002
4-3/M82	0.9813	1
5-3/M82	1.08591	1
6-2/M82	1.31083	1
6-3/M82	0.99165	1
7-1/M82	1.11794	0.598
7-2/M82	1.08845	1
9-3-2/M82	1.23671	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.19404	0.531
IL7-5/WTpooled	0.55674	1
IL7-3/WTpooled	1.28397	0.362
IL12-4/WTpooled	0.8861	0.71
IL1-4/WTpooled	1.1348	1
WT/WTpooled	0.97646	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	1.09712	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02049	0.921
DC3000/delta hrp 6h	0.88611	0.95
DC3000/delta hrp 12h	0.92541	1
DC3000/delta hrp 24h	1.03334	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.36678	0.076
DC3000 delta B/DC3000 delta AB	1.10024	0.498

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14205	1
Exp 36h	1.31237	1
Exp 60h	1.07322	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95265	1
Var 0h	0.97657	1
Var 12h I row2-row1	1.12561	0.348
Var 12h NI row2-row1	1.12665	0.649
Var 36h I row2-row1	1.00344	1
Var 36h NI row2-row1	1.08545	0.482
Var 60h I row2-row1	0.7732	0.292
Var 60h NI row2-row1	0.91442	0.932
Time course 0hI-0hNI	1.06105	0.867
Time course 12hI-12hNI	1.2952	0.019
Time course 36hI-36hNI	1.46849	0.007
Time course 60hI-60hNI	1.67778	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)	1.10441	0.511
transgenic ySAMdc/azygous control (breaker)	0.82848	0.251
transgenic ySAMdc/azygous control (red)	0.83801	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8723	0.065

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76273	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00531	1
Manapal/WT (break)	0.94754	1
Manapal/WT (red)	1.50367	0.142