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Table 1 The 44 families of animal bHLH defined by our phylogenetic analyses

From: Phylogenetic analysis of the human basic helix-loop-helix proteins

Family name Number of worm genes Number of fly genes Number of mouse genes Number of human genes Number of sea squirt genes Number of pufferfish genes Group
Achaete-Scute a 4 4 2 2 0 3 A
Achaete-Scute b 1 0 1 3 1 3 A
MyoD 1 1 4 4 1 1 A
E12/E47 1 1 4 6 1 1 A
Neurogenin 1 1 3 3 1 2 A
NeuroD 1 0 4 4 0 5 A
Atonal 1 3 2 2 1 4 A
Mist 0 1 1 1 1 0 A
Beta3 1 or 2* 1 2 2 0 2 A
Oligo 0 or 1* 0 3 3 0 3 A
Net 1 1 1 1 1 0 A
Mesp 0 1 3 4 1 2 A
Twist 1 1 2 1 0 3 A
Paraxis 0 1 2 1 0 2 A
MyoR 1 1 2 4 0 3 A
Hand 1 1 2 2 0 1 A
PTFa 0 1 1 1 0 1 A
PTFb 1 2 0 1 0 2 A
SCL 0 1 4 3 0 1 A
NSCL 1 1 2 2 0 1 A
SRC 0 1 3 3 0 2 B
Figa 0 0 1 1 1 0 B
Myc 0 1 4 5 0 3 B
Mad 1 0 4 5 1 or 2 0 B
Mnt 0 1 1 1 0 or 1† 0 B
Max 2 1 1 1 0 1 B
USF 1 1 2 3 0 1 B
MITF 1 0 4 5 0 2 B
SREBP 1 1 2 2 0 2 B
AP4 1 1 1 1 0 0 B
MLX 0 or 1§ 1 1 2 0 3 B
TF4 0 or 1§ 1 1 2 1 1 B
Clock 1 3 2 2 0 1 C
ARNT 1 1 2 2 1 2 C
Bmal 0 1 1 2 0 2 C
AHR 1 2 1 4 0 1 C
Sim 0 to 1 1 2 or 3 2 or 3 1 or 2 4 or 5 C
Trh 0 to 1 1 1 or 2 1 or 2 0 or 1 0 or 1 C
HIF 1 to 2 1 3 or 4 3 or 4 0 or 1 2 or 3 C
Emc 0 1 4 5 0 4 D
Hey# 0 2 2 5 1 2 E
Hairy# 0 3 1 2 1 4 E
E (spl) # 1 8 8 8 1 8 E
COE 1 1 4 4 0 0 F
Orphans 6 1 0 3 0 0 No
  1. Families have been named according to the name (or its common abbreviation) of the first discovered or best-known member of the family. The number of members per family in worm, fly and human (complete genomes) as well as in mouse, sea squirt, and pufferfish (uncompleted genomes) is reported. Each family has been tentatively assigned to a high-order group using the classification of Atchley and Fitch [6] and Ledent and Vervoort [8]. Genes that cannot be assigned to any families are categorized as 'orphan' genes. *Beta3 and Oligo are closely related families, one C. elegans gene (F38C2.2) belongs to the Beta3 family while another (DY3.3) is equally related to both Beta3 and Oligo families. Mad and Mnt are closely related families, one Ciona gene (Not7) belongs to the Mad family while another (LQW20007) is equally related to both Mad and Mnt families. These two families also include yeast genes. §TF4 and Mlx are closely related families, one C. elegans gene (T20B12.6) is equally related to both families. The Hif, Sim, and Trh families form a strongly supported monophyletic group (bootstrap value, 95%). A few genes that are included in this group cannot be clearly related to one of the three families (see Additional data for details). #The Hey, Hairy and Enhancer of split families genes form a well-supported monophyletic group (group E; see Figure 1). Two clear families (Hairy and Hey families) with high bootstrap support emerge from this group. All the remaining sequences have been grouped in a single family (named Enhancer of split), which has no real phylogenetic support. A phylogenetic tree of the group can be found in the Additional data.