BioMed Research International

Research Article

Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

Table 1

Information of the Xenopus tropicalis 105 bHLH transcription factors.


bHLH family	Gene name	Homo sapiens orthologous gene			Protein accession^c	Genome contig^d
bHLH family	Gene name	Name	MLE bootstrap value (%)^a	BI posterior probability (%)^b	Protein accession^c	Genome contig^d

ASCa	Xsash1	Hash1 (ASCL1)	89	99	XP_002944648.1	NW_003169609.1
ASCa	Xsash2	Hash2	n/m*	99	XP_002940290.1	NW_003163913.1
ASCb	Xsash3	Hash3 (ASCL3)	90	100	XP_002940370.1	NW_003163927.1
MyoD	Myf3	Myf3	96	94	NP_988972.1	NW_003166075.1
MyoD	Myf4	Myf4	94	100	NP_001016725.1	NW_003163495.1
MyoD	Myf5	Myf5	n/m	76	NP_988932.1	NW_003163331.1
MyoD	Myf6	Myf6	82	95	NP_001017160.1	NW_003163331.1
E12/E47	E2A	E2A	99	53	NP_001093743.1	NW_003163736.1
E12/E47	TCF3	TCF3	76	88	XP_002940299.1	NW_003163915.1
E12/E47	TCF4	TCF4	76	n/m*	NP_001096226.2	NW_003163423.1
Ngn	Xsath4c	Hath4c	83	78	NP_001116895.1	NW_003163503.1
NeuroD	NDF1 (neurod1)	NDF1 (NEUROD1)	n/m	n/m*	NP_001090868.1	NW_003163341.1
NeuroD	NDF2	NDF2 (NEUROD2)	65	63	NP_001072486.1	NW_003163936.1
NeuroD	Xsath2	Hath2	79	80	NP_001072273.1	NW_003163914.1
NeuroD	Xsath3	Hath3	97	99	NP_001124513.1	NW_003163487.1
Mist1	Mist1	Mist1	99	100	XP_002931994.1	NW_003163340.1
Beta3	Beta3a	Beta3a	70	53	XP_002944506.1	NW_003167409.1
Beta3	Beta3b	Beta3b	77	94	NP_001072933.1	NW_003163515.1
Oligo	Oligo1	Oligo1	97	100	XP_002938497.1	NW_003163700.1
Oligo	Oligo2	Oligo2	76	73	XP_002938491.1	NW_003163700.1
Oligo	Oligo3	Oligo3	83	90	NP_001008191.1	NW_003163713.1
Oligo	Oligo4	Oligo1 Oligo2 Oligo3	n/m	n/m	NP_001039180.1	NW_003163795.1
Net	Xsath6	Hath6	100	100	XP_002937330.1	NW_003163606.1
Mesp	Mesp1	Mesp1 Mesp2 pMesp1	n/m	n/m	NP_001039184.1	NW_003163348.1
Mesp	Mesp2	Mesp1 Mesp2 pMesp1	n/m	n/m	NP_001016653.1	NW_003163348.1
Mesp	pMespo	pMesp1	99	100	NP_001039104.1	NW_003163426.1
Twist	Twist1	Twist1	91	83	NP_989415.1	NW_003163378.1
Twist	Twist2	Twist2	98	100	NP_001096679.1	NW_003163487.1
Paraxis	Paraxis	Paraxis	62	83	NP_001016506.1	NW_003165117.1
Paraxis	Sclerax1	Sclerax	96	99	XP_002942929.1	NW_003164455.1
Paraxis	Sclerax2	Sclerax	74	59	XP_002937913.1	NW_003163647.1
MyoRa	MyoRa1	MyoRa1	63	60	NP_001096235.1	NW_003163586.1
MyoRa	MyoRa2	MyoRa2	n/m	62	NP_001103518.1	NW_003163498.1
MyoRb	MyoRb1	MyoRb1	78	94	GNOMON∣93674.p^e (ab initio protein)	NW_003164157.1
MyoRb	MyoRb2	MyoRb2	55	95	GNOMON∣522504.p^e (ab initio protein)	NW_003163470.1
Hand	Hand1	Hand1	94	100	NP_001016743.1	NW_003163350.1
Hand	Hand2	Hand2	99	55	NP_001093695.1	NW_003163380.1
PTFa	PTFa	PTFa	99	100	NP_001095279.1	NW_003163378.1
PTFb	PTFb	PTFb	91	100	XP_002933181.1	NW_003163373.1
SCL	Tal1	Tal1	77	62	NP_001135468.1	NW_003163327.1
SCL	Tal2	Tal2	72	76	XP_002934026.1	NW_003163404.1
SCL	Lyl1	Lyl1	86	97	XP_002939165.1	NW_003163774.1
NSCL	NSCL1	NSCL1	99	100	XP_002937307.1	NW_003163605.1
SRC	SRC1	SRC1	82	97	NP_001106383.1	NW_003163796.1
SRC	SRC2	SRC2	97	100	NP_001135631.1	NW_003163586.1
SRC	SRC3	SRC3	80	97	XP_002933204.1	NW_003163374.1
Figα	Figα	Figα	92	100	NP_001016342.1	NW_003163469.1
MYC	l-Myc	L-Myc	71	65	NP_001011144.1	NW_003164143.1
MYC	n-Myc	n-Myc	n/m	98	NP_989390.1	NW_003163721.1
MYC	v-Myc	v-Myc	91	99	NP_001006874.1	NW_003163866.1
Mad	Mxi1	Mxi1	85	97	NP_001008129	NW_003180496.1 NW_003163820.1
Mad	Mad1	Mad1	n/m	88	NP_001072228.1	NW_003163469.1
Mad	Mad3	Mad3	99	100	NP_001017299.1	NW_003163577.1
Mad	Mad4	Mad4	89	100	NP_001096239.1	NW_003164437.1
Mnt	Mnt	Mnt	n/m	97	NP_001135494.1	NW_003163468.1
MAX	MAX	MAX	90	100	NP_001008208.1	NW_003163599.1
USF	USF1	USF1	92	99	NP_001096236.1	NW_003168160.1
USF	USF2	USF2	n/m	60	NP_001007857.1	NW_003163677.1
USF	USF3	USF3	85	99	NP_001120597.1	NW_003164188.1
MITF	MITF	MITF	n/m	n/m	NP_001093747.1	NW_003163951.1
MITF	TFEb	TFEb	84	100	NP_001072648.1	NW_003163367.1
MITF	TFEc	TFEc	66	99	XP_002935013.1	NW_003163447.1
MITF	TFE3	TFE3	85	78	XP_002944430.1	NW_003166883.1
SREBP	SREBP1a	SREBP1	88	99	XP_002935886.1	NW_003163500.1
SREBP	SREBP1b	SREBP1	88	99	XP_002935887.1	NW_003163500.1
SREBP	SREBP1c	SREBP1	88	99	XP_002944649.1	NW_003169615.1 NW_003163500.1
SREBP	SREBP2	SREBP2	n/m	67	NP_001116910.1	NW_003163395.1
AP4	AP4	AP4	71	98	NP_001123841.1	NW_003163353.1
Mlx	MondoA	MondoA	89	100	NP_001090682.1	NW_003163637.1
TF4	TF4	TF4	88	100	GNOMON:712044.p^e (ab initio protein)	NW_003164277.1, NW_003164157.1
Clock	Clock	Clock	99	100	NP_001122127.1	NW_003163433.1
ARNT	ARNT1	ARNT1	n/m	n/m	NP_001116925.1	NW_003163477.1
ARNT	ARNT2	ARNT2	100	n/m	NP_001093686.1	NW_003163348.1
Bmal	Bmal2	Bmal2	63	100	NP_001096298.1	NW_003164805.1
AHR	AHR1	AHR1	92	99	XP_002933348.1	NW_003163378.1
AHR	AHR2	AHR2	91	100	XP_002935182.1	NW_003163457.1
Sim	Sim1	Sim1	n/m*	98	XP_002932187.1	NW_003163345.1
Sim	Sim2	Sim2	89	99	XP_002941575.1	NW_003164120.1
Trh	NPAS3	NPAS3	n/m	70	NP_001072647.1	NW_003163363.1
HIF	Hif1α	Hif1α	99	n/m	NP_001011165.1	NW_003163817.1
HIF	EPAS1	EPAS1	79	94	NP_001005647.1	NW_003163351.1
Emc	Id2	Id2	78	90	NP_988885.1	NW_003163451.1
Emc	Id3	Id3	79	98	NP_001016271.1	NW_003163432.1
Emc	Id4	Id4	86	54	NP_001004839.1	NW_003163385.1
Hey	Herp1	Herp1	83	97	NP_001007911.1	NW_003163551.1
Hey	Herp2	Herp2	86	92	XP_002936042.1	NW_003163507.1
Hey	HEYL	HEYL	98	100	XP_002934312.1	NW_003163416.1
H/E(spl)	Dec2	Dec2	99	n/m	NP_001027504.1	NW_003163993.1
H/E(spl)	Hes1a	Hes1	n/m	81	NP_001011194.1	NW_003163571.1
H/E(spl)	Hes1b	Hes1	n/m	81	NP_988870.1	NW_003163533.1
H/E(spl)	Hes5a	Hes5	n/m*	61	NP_001037880.1	NW_003163546.1
H/E(spl)	Hes5b	Hes5	n/m*	61	NP_001037974.1	NW_003163546.1
H/E(spl)	Hes5c	Hes5	n/m*	100	NP_001039178.1	NW_003163399.1
H/E(spl)	Hes5d	Hes5	n/m*	100	NP_001037951.1	NW_003163399.1
H/E(spl)	Hes5e	Hes5	n/m*	82	NP_001107462.1	No finding
H/E(spl)	Esr9	Hes5	n/m*	100	NP_001037989.1	NW_003163399.1
H/E(spl)	Hes6	Hes6	n/m	n/m	NP_001072210.1	NW_003163381.1
H/E(spl)	Hes7a	Hes7	73	97	NP_001039166.1	NW_003164377.1
H/E(spl)	Hes7b	Hes7	86	100	NP_001107508.1	NW_003164377.1
Coe	EBF1	EBF1	n/m	51	XP_002939654.1	NW_003163834.1
Coe	EBF2	EBF2	91	97	NP_989200.1	NW_003163356.1
Coe	EBF3	EBF3	91	66	XP_002932694.1	NW_003163358.1
Coe	EBF4	EBF4	91	66	XP_002932695.1	NW_003163358.1
Orphan	Orphan1	Orphan1	86	100	XP_002938975.1	NW_003163749.1
Orphan	Orphan4	Orphan4	94	100	XP_002943245.1	NW_003164609.1

Xenopus tropicalis bHLH genes were named according to their human orthologous genes’ names (or common abbreviations) and the referred nomenclature was mainly from the tables and additional tables provided by Ledent et al. [4] and Simionato et al. [6]. Bootstrap values were converted from phylogenetic analyses with human bHLH sequences using BI and MLE algorithm, respectively. MLE bootstrap value^a refers to the result from maximum likelihood estimate in phylogenetic analysis, and BI posterior probability^b refers to the result from BI in phylogenetic analysis. The numbers in the phylogenetic trees are converted into percentages. The accession numbers were retrieved from the following resources; this sequence was verified by many EST TBLASTN search hits, such as EG651417.1 and CX503003.2 (EST accession number). These numbered as “NP” were from the RefSeq protein database and those numbered as “XP” were from the Build protein database. Notes in the brackets are also gene symbols according to records in NCBI and Xenbase. All of the bHLH genes are organized in the order of bHLH families manifested in Table 1 of Ledent et al. [4]. The question mark means no matching; mark n/m* means no monophyletic group with single particular orthologous gene sequences, but formed a monophyletic group with two or more orthologous gene sequences of the family; mark n/m denotes the case of lower bootstrap value estimated less than 50%.The accession numbers were retrieved from the ab initio protein database.