GenFam: gene family‐based classification and functional enrichment analysis

Renesh Bedre        5 minute read

What is GenFam?

  • GenFam is a new computational approach which allows annotation, classification, and enrichment of genes based on their gene family in plants genome. For example, GenFam can be useful to identify overrepresented differentially expressed genes obtained from RNA‐seq experiment (read GenFam paper for more details)
  • GenFam and its integrated database comprises of 384 unique gene families and supports gene family analyses for 60 plant genomes.
  • GenFam empowers users to readily interpret information of gene families (e.g., WRKY and bZIP) rather than GO terms or hierarchy alone in their queries, and move forward to selecting favorite overrepresented genes (or families) for downstream studies and interpretation.
  • Here, I have described how to use GenFam as command line interface (CLI). The online version of GenFam can be found here

How to use GenFam as command line interface (CLI)?

GenFam classification and enrichment analysis for cotton genes

# I am using interactive python interpreter (Python 3.8.5)
# you must have active internet connection for GenFam analysis
>>> from bioinfokit.analys import genfam
# perform genfam analysis on downloaded G.raimondii dataset
>>> res = genfam()
>>> res.fam_enrich(id_file='grai_id.txt', species='grai', id_type=1) 
# by default fam_enrich will use Fisher exact test and Benjamini-Hochberg FDR method
# get enriched gene families
>>> res.df_enrich
                                          Gene Family Short name       p value           FDR
0                                     MYB gene family        MYB  2.152548e-30  1.291529e-28
17                               Expansin gene family   Expansin  2.528412e-20  7.585235e-19
1                                    WRKY gene family       WRKY  3.259473e-18  4.942421e-17
16                GDSL-like lipase (GELP) gene family       GELP  3.294948e-18  4.942421e-17
2   Basic helix-loop-helix (bHLH) gene family gene...       bHLH  2.889523e-17  3.467428e-16
13                Cellulose synthase (CS) gene family         CS  4.071289e-12  4.071289e-11
14        Glutathione S-transferase (GST) gene family        GST  1.786892e-09  1.531622e-08
4                                Homeobox gene family   Homeobox  1.131515e-08  8.310631e-08
20         Kunitz Trypsin Inhibitor (KTI) gene family        KTI  1.246595e-08  8.310631e-08
24                                    GH3 gene family        GH3  7.769853e-07  4.661912e-06
18                                   SAUR gene family       SAUR  8.787804e-07  4.793347e-06
8       Late embryogenesis abundant (LEA) gene family        LEA  4.981083e-06  2.490542e-05
12   Chalcone and stilbene synthase (CSS) gene family        CSS  6.766939e-06  3.123203e-05
23                 Auxin transport (AUXT) gene family       AUXT  4.088460e-05  1.728157e-04
5                Glycoside hydrolase (GH) gene family         GH  4.320394e-05  1.728157e-04
21                   Thaumatin-like (TLP) gene family        TLP  5.855903e-05  2.195964e-04
27          Glycosyltransferase 61 (GT61) gene family       GT61  8.441974e-04  2.979520e-03
25      Phenylalanine ammonia lyase (PAL) gene family        PAL  1.098768e-03  3.662560e-03
10            Basic leucine zipper (bZIP) gene family       bZIP  1.192707e-03  3.766444e-03
11                    NADPH oxidase (NOX) gene family        NOX  1.357703e-03  4.073110e-03
19                     Lipoxygenase (LOX) gene family        LOX  2.056488e-03  5.875680e-03
28               Protein kinase (PK) gene superfamily         PK  3.250643e-03  8.865390e-03
3                               AP2/EREBP gene family  AP2/EREBP  6.056923e-03  1.575365e-02
26                Cytokinin oxidase (CKX) gene family        CKX  6.301461e-03  1.575365e-02
7          UDP-glycosyltransferases (UGT) gene family        UGT  1.252574e-02  3.006178e-02
6   Cysteine-rich secretory proteins, Antigen 5, a...        CAP  1.992329e-02  4.597683e-02
15                                  HSP20 gene family      HSP20  2.606746e-02  5.792769e-02
9             Glycosyltransferase 5 (GT5) gene family        GT5  3.031398e-02  6.495853e-02
22  Cysteine-rich receptor-like kinases (CRK) gene...        CRK  4.199360e-02  8.688330e-02

# enriched gene families and all gene families along with GO annotation will be saved in 
# fam_enrich_out.txt and fam_all_out.txt in the current working directory
# figure of enriched gene families (genfam_enrich.png) will also be saved

# get genfam analysis information
>>> res.genfam_info
                                     Parameter                     Value
0                         Total query gene IDs                       652
1                    Number of genes annotated                       518
2  Number of enriched gene families (p < 0.05)                        29
3                                Plant species  Gossypium raimondii v2.1
4              Statistical test for enrichment         Fisher exact test
5           Multiple testing correction method        Benjamini-Hochberg
6                           Significance level                      0.05

# if you are not sure about the type of gene IDs acceptable for GenFam, you can check it using check_allowed_ids
# function

>>> res.check_allowed_ids(species='grai')

Allowed ID types for  Gossypium raimondii v2.1 

 Phytozome locus:  Gorai.006G113100 
 Phytozome transcript:  Gorai.013G113000.1 
 Phytozome pacID:  26782432 


Enriched gene families figure,

GenFam classification and enrichment analysis for rice genes

>>> res.fam_enrich(id_file='osat_id.txt', species='osat', id_type=2) 
>>> res.df_enrich
                                          Gene Family Short name       p value           FDR
27                                Tubulin gene family    Tubulin  1.018099e-09  1.547510e-07
16               Glycoside hydrolase (GH) gene family         GH  3.405050e-09  2.587838e-07
7                       Core histone (CH) gene family         CH  4.670238e-07  2.366254e-05
9                                   Cupin gene family      Cupin  1.637162e-06  6.221217e-05
11   Fasciclin-like arabinogalactan (FLA) gene family        FLA  6.453438e-05  1.814660e-03
4                        Aquaporins (AQP) gene family        AQP  7.987808e-05  1.814660e-03
18                               Kinesins gene family   Kinesins  8.356985e-05  1.814660e-03
6                 Cellulose synthase (CS) gene family         CS  1.377311e-04  2.616891e-03
13                GDSL-like lipase (GELP) gene family       GELP  1.858720e-04  3.139171e-03
2            Aldehyde dehydrogenase (ADH) gene family        ADH  6.513123e-04  9.899947e-03
3                   Aminotransferase (AT) Gene Family         AT  8.690746e-04  1.200903e-02
0                                  14-3-3 gene family     14-3-3  9.966784e-04  1.262459e-02
15        Glutathione S-transferase (GST) gene family        GST  2.597434e-03  3.037000e-02
23  Papain-like cysteine proteases (PLCP) gene family       PLCP  4.697927e-03  5.100606e-02
21              Multicopper oxidase (MCO) gene family        MCO  5.686257e-03  5.762074e-02
17          Glycosyltransferase 75 (GT75) gene family       GT75  7.438912e-03  7.066967e-02
19            Malate dehydrogenases (MDH) gene family        MDH  8.891813e-03  7.773310e-02
25          Serine carboxypeptidase (SCP) gene family        SCP  9.205236e-03  7.773310e-02
12           Fatty acid hydroxylase (FAH) gene family        FAH  1.343143e-02  1.036782e-01
1                         ABC transporter gene family        ABC  1.402746e-02  1.036782e-01
10                               Expansin gene family   Expansin  1.432396e-02  1.036782e-01
14              Glutamine synthetase (GS) gene family         GS  1.705606e-02  1.127881e-01
22                    NADPH oxidase (NOX) gene family        NOX  1.706663e-02  1.127881e-01
26                   Thaumatin-like (TLP) gene family        TLP  1.954518e-02  1.237862e-01
5                  Auxin transport (AUXT) gene family       AUXT  2.344961e-02  1.370900e-01
28    UDP-glucuronate decarboxylase (UXS) gene family        UXS  2.344961e-02  1.370900e-01
20      Phenylalanine ammonia lyase (PAL) gene family        PAL  2.988103e-02  1.682191e-01
8                   Core cell cycle (CCC) gene family        CCC  4.239049e-02  2.301198e-01
24  S-adenosyl-L-homocysteine hydrolase (SAHH) gen...       SAHH  4.544742e-02  2.382072e-01


>>> res.genfam_info
                                     Parameter                       Value
0                         Total query gene IDs                         758
1                    Number of genes annotated                         460
2  Number of enriched gene families (p < 0.05)                          29
3                                Plant species  Oryza sativa v7_JGI (Rice)
4              Statistical test for enrichment           Fisher exact test
5           Multiple testing correction method          Benjamini-Hochberg
6                           Significance level                        0.05

# check allowed ID types for rice for genfam analysis
>>> res.check_allowed_ids(species='osat')

Allowed ID types for  Oryza sativa v7_JGI (Rice) 

 Phytozome locus:  LOC_Os01g10150 
 Phytozome transcript:  LOC_Os02g09740.2 
 Phytozome pacID:  24127097 

In addition, you can customize different parameters for GenFam analysis (check parameters and list of plant species supported by GenFam).

GenFam citation

  • Bedre R, Mandadi K. GenFam: A web application and database for gene family‐based classification and functional enrichment analysis. Plant Direct. 2019 Dec;3(12):e00191.

References

  • Dametto A, Sperotto RA, Adamski JM, Blasi ÉA, Cargnelutti D, de Oliveira LF, Ricachenevsky FK, Fregonezi JN, Mariath JE, da Cruz RP, Margis R. Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes. Plant Science. 2015 Sep 1;238:1-2.
  • Bedre R, Rajasekaran K, Mangu VR, Timm LE, Bhatnagar D, Baisakh N. Genome-wide transcriptome analysis of cotton (Gossypium hirsutum L.) identifies candidate gene signatures in response to aflatoxin producing fungus Aspergillus flavus. PLoS One. 2015 Sep 14;10(9):e0138025.

Last updated: October 10, 2020

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