Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

Carrillo, Alexander J.; Cabrera, Ilva E.; Spasojevic, Marko J.; Schacht, Patrick; Stajich, Jason E.; Borkovich, Katherine A.

doi:10.1186/s12864-020-07131-7

BMC Genomics

Table 2 Phenotype summary for 40 PAM clusters

From: Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

Cluster #	# Genes in cluster	% Mutants with same phenotype^a
Cluster #	# Genes in cluster	Basal hyphae growth rate	Aerial hyphae height	Conidial #	Conidial morph-ology	Protoperi-thecial #	Protoperi-thecial morph-ology	Peri-thecial #	Peri-thecial morph-ology	Asco-spore #	Asco-spore morph-ology
1	28	75% Normal Average	57% Normal High	93% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal
2	10	90% Reduced	80% Reduced	100% Reduced	100% Normal	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
3	171	94% Normal Low	95% Normal Average	99% Normal	100% Normal	100% Normal	100% Normal	100% Normal	99% Normal	100% Normal	100% Normal
4	82	88% Normal Average	85% Normal Average	98% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal
5	73	100% Slightly Reduced	93% Reduced	100% Normal	100% Normal	99% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal
6	23	100% Reduced	96% Reduced	100% Normal	100% Normal	96% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal
7	130	100% Slightly Reduced	96% Normal Average	99% Normal	100% Normal	100% Normal	100% Normal	100% Normal	99% Normal	99% Normal	100% Normal
8	38	100% Reduced	100% Reduced	97% Normal	97% Normal	97% Normal	100% Normal	97% Normal	100% Normal	100% Normal	100% Normal
9	82	80% Normal Low	95% Reduced	100% Normal	100% Normal	100% Normal	99% Normal	99% Normal	100% Normal	95% Normal	100% Normal
10	8	62% Severely Reduced	75% Normal Average	75% Normal	100% Normal	88% Normal	100% Normal	62% Normal	88% Normal	75% Normal	100% Normal
11	8	50% Slightly Reduced	88% Reduced	100% Normal	100% Normal	100% Normal	75% Normal	88% Not Formed	88% Not Formed	100% Not Formed	100% Not Formed
12	8	88% Reduced	88% Reduced	100% Reduced	88% Normal	62% Normal	50% Normal	88% Not Formed	88% Not Formed	100% Not Formed	100% Not Formed
13	12	50% Reduced	58% Reduced	75% Reduced	92% Normal	92% Reduced	100% Normal	92% Reduced	92% Normal	83% Reduced	83% Normal
14	9	Varied	89% Normal Average	89% Normal	100% Normal	89% Normal	100% Normal	67% Normal	78% Normal	100% Not Formed	100% Not Formed
15	77	100% Slightly Reduced	96% Normal Average	100% Normal	100% Normal	100% Normal	100% Normal	97% Normal	100% Normal	99% Normal	100% Normal
16	21	Varied	67% Normal Average	95% Normal	95% Normal	86% Normal	90% Normal	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
17	12	100% Severely Reduced	92% Reduced	92% Normal	83% Normal	92% Normal	100% Normal	100% Normal	92% Normal	92% Normal	92% Normal
18	8	100% Severely Reduced	88% Reduced	75% Normal	88% Normal	88% Not Formed	88% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
19	25	52% Reduced	100% Increased	96% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	96% Normal	100% Normal
20	19	74% Severely Reduced	100% Reduced	84% Normal	95% Normal	95% Normal	95% Normal	100% Normal	100% Normal	89% Normal	100% Normal
21	42	100% Slightly Reduced	100% Reduced	100% Normal	100% Normal	100% Normal	98% Normal	100% Normal	100% Normal	100% Normal	100% Normal
22	32	100% Reduced	84% Normal Average	97% Normal	100% Normal	97% Normal	100% Normal	97% Normal	100% Normal	97% Normal	97% Normal
23	11	82% Reduced	91% Reduced	91% Normal	100% Normal	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
24	13	85% Reduced	85% Reduced	92% Normal	92% Normal	92% Normal	62% Normal	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
25	11	91% Reduced	100% Severely Reduced	55% Reduced	100% Normal	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
26	15	67% Slightly Reduced	100% Severely Reduced	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal	97% Normal	100% Normal
27	15	Varied	60% Normal Average	100% Normal	100% Normal	80% Normal	100% Normal	87% Normal	87% Normal	93% Reduced	100% Normal
28	15	67% Reduced	100% Increased	80% Normal	100% Normal	93% Normal	93% Normal	100% Normal	93% Normal	87% Normal	100% Normal
29	9	67% Slightly Reduced	78% Reduced	89% Normal	100% Normal	89% Normal	89% Normal	78% Reduced	89% Normal	100% Not Formed	100% Not Formed
30	7	100% Severely Reduced	100% Severely Reduced	Varied	71% Normal	100% Normal	100% Normal	57% Normal	86% Normal	Varied	Varied
31	36	100% Reduced	92% Normal Average	97% Normal	100% Normal	100% Normal	97% Normal	94% Normal	100% Normal	94% Normal	100% Normal
32	9	56% Slightly Reduced	89% Reduced	100% Reduced	100% Normal	89% Normal	100% Normal	100% Normal	100% Normal	100% Normal	100% Normal
33	6	50% Reduced, 50% Severely Reduced	67% Normal Average	67% Normal	67% Normal	83% Reduced	100% Normal	83% Reduced	67% Abnorm-al Beaks	83% Not Formed	83% Not Formed
34	12	67% Reduced	83% Normal Average	83% Normal	75% Normal	92% Not Formed	92% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed
35	10	60% Slightly Reduced	50% Normal Average	100% Normal	100% Normal	100% Reduced	90% Normal	90% Reduced	100% Normal	60% Normal	100% Normal
36	33	Varied	100% Increased	88% Normal	100% Normal	100% Normal	100% Normal	100% Normal	94% Normal	100% Normal	100% Normal
37	13	69% Reduced	85% Reduced	92% Normal	100% Normal	92% Normal	92% Normal	85% Normal	77% Normal	100% Reduced	100% Normal
38	9	67% Reduced	100% Severely Reduced	89% Normal	100% Normal	89% Normal	89% Normal	89% Normal	100% Normal	89% Normal	100% Normal
39	5	80% Reduced	60% Reduced	80% Normal	100% Normal	100% Normal	100% Normal	100% Normal	Varied	100% Not Formed	100% Not Formed
40	21	100% Severely Reduced	100% Severely Reduced	76% Reduced	90% Normal	90% Not Formed	90% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed	100% Not Formed

^aThe value in the cell is the percentage of mutants with the indicated majority phenotype. Varied indicates that no one phenotype was present in more than 50% of the mutants. Normal range for growth rate is 75–85 mm/day. 75–77.5 = Normal Low; 77.6–82.5 = Normal Average; 82.6–85 = Normal High; 65–74.9 = Slightly Reduced; 40–64.9 = Reduced; < 40 = Severely Reduced; > 85 = Increased. Normal range for aerial hyphae height is 30-45 mm. 35.1–39.9 = Normal Average; 30–35 = Normal Low; 40–45 = Normal High; 25–29 = Slightly Reduced; 15–24.9 = Reduced; < 15 = Severely Reduced; > 45 = Increased

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