Tables in the chili database

Description of (some) of the tables in the chili database.
Variables shared by more than one table are highlited in  bold purple.

seq

Sequences (transcripts) assembled from the experiment

Field Description
Type
seq_id Numeric Sequence Identifier
int(11)
seq_name Oficial name of the sequence
varchar(20)
seq Sequence itself
varchar(20000)

seq_ident

Identification of sequences (source and description)

Field Description
Type
seq_id Numeric Sequence Identifier int(11)
seq_name Oficial name of the sequence varchar(20)
contig Contig to which the sequence belongs
varchar(30)
BLAST_DB Database used for identification
varchar(30)
gene Identifier Gene (gene_id in expression)
varchar(30)
description Description of identifier gene
varchar(500)
length_alin_bp Length of the full alignment in base pairs
int(5)
perc_align Maximum percentage of alignment
float
bitscore Score in bits of alignment
int(5)

info_seq

Information about sequences (length and % of GC)

Field Description
Type
seq_id Numeric Sequence Identifier int(11)
seq_name Oficial name of the sequence varchar(20)
contig Contig to which the sequence belongs varchar(20)
c_num Number of component (in seq_name)
int(1)
seq_num Number of sequence (in seq_name)
int(3)
lenght Length of the sequence (in bp)
int(6)
p_gc Percentage of GC
double


expression

Expression level per gene and library

Field Description
Type
id_expressed Numeric identifier
int(11)
id_gene Gene identifier (gene in  seq_ident)
varchar(30)
D10R1 Expression at 10 DAA in replicate 1
decimal(32,0)
D10R2 Expression at 10 DAA in replicate 2
decimal(32,0)
D20R1 Expression at 20 DAA in replicate 1 decimal(32,0)
D20R2 Expression at 20 DAA in replicate 2
decimal(32,0)
D40R1 Expression at 40 DAA in replicate 1
decimal(32,0)
D40R2 Expression at 40 DAA in replicate 2
decimal(32,0)
D60R1 Expression at 60 DAA in replicate 1 decimal(32,0)
D60R2 Expression at 60 DAA in replicate 2
decimal(32,0)

expressTPMround

Expression level in Transcripts Per Million (rounded) per gene and treatment

Field Description
Type
id_expressed Numeric identifier int(11)
id_gene Gene identifier (gene in  seq_ident)
varchar(30)
D10 Average Expression at 10 DAA in TPM
double(17,0)
D20 Average Expression at 20 DAA in TPM double(17,0)
D40 Average Expression at 40 DAA in TPM double(17,0)
D60 Average Expression at 60 DAA in TPM double(17,0)
I10to20 Indicator of significant change from 10 to 20 DAA
int(1)
I20to40 Indicator of significant change from 20 to 40 DAA int(1)
I40to60 Indicator of significant change from 40 to 60 DAA int(1)

annotBPexpress

Annotation by Biological Process (BP) from Gene Ontology

Field Description
Type
id_expressed Numeric identifier of gene
int(11)
id_gene Gene identifier (gene in  seq_ident) varchar(30)
description Brief description of the GO term
varchar(5000)
id_BPdesc Numeric identifier of the GO term
int(4)

annotCCexpress

Annotation by Cellular Component (CC) from Gene Ontology

Field Description
Type
id_expressed Numeric identifier of gene int(11)
id_gene Gene identifier (gene in  seq_ident) varchar(30)
description Brief description of the GO term varchar(5000)
id_CCdesc
Numeric identifier of the GO term
int(4)

annotMFexpress

Annotation by Molecular Function (MF) from Gene Ontology

Field Description
Type
id_expressed Numeric identifier of gene int(11)
id_gene Gene identifier (gene in  seq_ident) varchar(30)
description Brief description of the GO term varchar(5000)
id_MFdesc Numeric identifier of the GO term int(4)

annotKegPathExpress

Annotation by KEG metabolic pathway

Field Description
Type
id_expressed Numeric identifier of gene int(11)
id_gene Gene identifier (gene in  seq_ident) varchar(30)
pathway_hit Description of metabolic pathway
varchar(1000)
id_KPdesc Numeric identifier of the metabolic pathway int(4)

DisDE

Summary of statistical results from the analysis

Field Description
Type
id Numerical identifier
int(11)
gene_id Gene identifier (gene in  seq_ident) varchar(30)
q_Gb Q value for the Gb test (all treatments)
double
q_Gw Q value for the Gw test (all treatments) double
q_F Q value for the F test (all treatments) double
q_DE Q value for differential expression (all treatments) double
D_Gb Indicator of discovery by the Gb test
int(1)
D_F Indicator of discovery by the F test int(1)
D_OD Indicator of over disperssion int(1)
D_DE Indicator of discovery of Differential Expression (all treatments)
int(1)
useGb Indicator of use of qGb in DE test
int(1)
q_Gb1_2 Q value for the Gb test (treatments 10 vs 20) double
q_Gw1_2 Q value for the Gw test (treatments 10 vs 20) double
q_F1_2 Q value for the F test (treatments 10 vs 20) double
q_DE1_2 Q value for DE test (treatments 10 vs 20) double
D_Gb1_2 Indicator of discovery by the Gb test (treatments 10 vs 20) int(1)
D_F1_2 Indicator of discovery by the F test (treatments 10 vs 20) int(1)
D_OD1_2 Indicator of over dispersion (treatments 10 vs 20) int(1)
D_DE1_2 Indicator of discovery of Differential Expression (treatments 10 vs 20) int(1)
useGb1_2 Indicator of use of qGb in DE test (treatments 10 vs 20) int(1)
q_Gb2_4 Q value for the Gb test (treatments 20 vs 40) double
q_Gw2_4 Q value for the Gw test (treatments 20 vs 40) double
q_F2_4 Q value for the f test (treatments 20 vs 40) double
q_DE2_4 Q value for differential expression (treatments 20 vs 40) double
D_Gb2_4 Indicator of discovery by the Gb test (treatments 20 vs 40) int(1)
D_F2_4 Indicator of discovery by the F test (treatments 20 vs 40) int(1)
D_OD2_4 Indicator of over dispersiion (treatments 20 vs 40) int(1)
D_DE2_4
Indicator of discovery of Differential Expression (treatments 20 vs 40)
int(1)
useGb2_4 Indicator of use of qGb in DE test (treatments 20 vs 40) int(1)
q_Gb4_6 Q value for the Gb test (treatments 40 vs 60) double
q_Gw4_6 Q value for the Gw test (treatments 40 vs 60) double
q_F4_6 Q value for the F test (treatments 40 vs 60) double
q_DE4_6 Q value for differential expression (treatments 40 vs 60) double
D_Gb4_6 Indicator of discovery by the Gb test (treatments 40 vs 60) int(1)
D_F4_6 Indicator of discovery by the F test (treatments 40 vs 60) int(1)
D_OD4_6 Indicator of over dispersion (treatments 40 vs 60) int(1)
D_DE4_6 Indicator of discovery of differential expression (treatments 40 vs 60) int(1)
useGb4_6 Indicator of use of qGb in DE test (treatments 40 vs 60) int(1)

discoveries

Summary of gene expression discoveries

Field Description
Type
id_gene Gene identifier (gene in  seq_ident) varchar(30)
D10 rounded mean expression in treatment D10 (TPM)
double(17,0)
D20 rounded mean expression in treatment D20 (TPM) double(17,0)
D40 rounded mean expression in treatment D40 (TPM) double(17,0)
D60 rounded mean expression in treatment D60 (TPM) double(17,0)
D_DE Indicator of discovery of Differential Expression (all treatments) int(1)
I10to20 Signed indicator of Differential Expression between D10 and D20
bigint(13)
I20to40 Signed indicator of Differential Expression between D20 and D40 bigint(13)
I40to60 Signed indicator of Differential Expression between D40 and D60 bigint(13)
ch10to20 Net significant expression change between D10 and D20 in TPM
int(10)
ch20to40 Net significant expression change between D20 and D40 in TPM int(10)
ch40to60 Net significant expression change between D40 and D60 in TPM int(10)

desc_tables

Description of the tables in the chili database

Field Description
Type
chili_table Name of the table
varchar(30)
description Description of the table
varchar(1500)

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