Protein classes - The Human Protein Atlas

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Protein classesⁱ
The protein class page contains a selection of gene lists used to stratify the proteome. Each table shows the total number of genes as well as the number of genes with antibodies for all classes. Clicking on one of these two links retrieves a search result with the selection of genes belonging to the class, along with additional data. For each class, where applicable, there is also a link to the original source of the gene list. A number of classes contain a selection of subclasses which unfolds when the parent class (shown in bold and with arrows) is clicked. The subclasses contain the same features as the parent class but may have different sources. Some subclasses (marked with an asterisk) are not included in the total number of genes for the parent class.

All protein classes have been categorized into three different tables: "Function and compartment based", "Disease and drug related", and "Evidence based".

Protein class	No of genes	No of genes with antibodies	Source
Function and compartment basedⁱ The "Function and compartment based" table contains functional classes of proteins such as transcription factors and enzymes, as well as proteins located to specific compartments of the cell, such as the predicted membrane proteins. The "Predicted membrane proteins" subclasses have been previously described in more detail in a publication. The class "Secreted proteins predicted by MDSEC" includes proteins not containing transmembrane regions and having a signal peptide predicted by at least two of the three signal peptide prediction methods SignalP4.0, Phobius, and SPOCTOPUS.
Enzymes	3465	3235
ENZYME proteins	3225	3030	ENZYME
Oxidoreductases	401	372	ENZYME
Transferases	1493	1404	ENZYME
Hydrolases	1047	979	ENZYME
Lyases	130	123	ENZYME
Isomerase	103	101	ENZYME
Ligase	105	104	ENZYME
Peptidases	496	444	UniProt/Merops
Aspartic-type peptidases	17	16	UniProt/Merops
Cysteine-type peptidases	159	152	UniProt/Merops
Metallopeptidases	133	114	UniProt/Merops
Serine-type peptidases	163	140	UniProt/Merops
Threonine-type peptidases	20	18	UniProt/Merops
Kinases	502	480	UniProt
AGC Ser/Thr protein kinases	56	55	UniProt
Tyr protein kinases	88	84	UniProt
TKL Ser/Thr protein kinases	34	30	UniProt
STE Ser/Thr protein kinases	55	55	UniProt
RGC receptor guanylate cyclase kinases	5	2	UniProt
NEK Ser/Thr protein kinases	11	11	UniProt
CMGC Ser/Thr protein kinases	61	58	UniProt
CK1 Ser/Thr protein kinases	13	13	UniProt
CAMK Ser/Thr protein kinases	73	70	UniProt
Atypical kinases	27	26	UniProt
CD markers	373	322	UniProt
Blood group antigen proteins	31	24	UniProt
Nuclear receptors	49	44	NucleaRDB
Transporters	1317	1149	TCDB
Transporter channels and pores	428	365	TCDB
Electrochemical Potential-driven transporters	396	353	TCDB
Primary Active Transporters	141	131	TCDB
Transport Electron Carriers	13	10	TCDB
Accessory Factors Involved in Transport	155	136	TCDB
Ribosomal proteins	177	174	UniProt
G-protein coupled receptors	752	382	UniProt
Family 3 (C) receptors	21	17	UniProt
GPCRs excl olfactory receptors	392	282	UniProt
Adenosine and adenine nucleotide receptors	17	16	UniProt
Chemokines and chemotactic factors receptors	29	24	UniProt
Lysolipids receptors	14	11	UniProt
Odorant/olfactory and gustatory receptors	360	100	UniProt
Opsins	9	5	UniProt
Serotonin receptors	12	9	UniProt
Family 2 (B) receptors	47	40	UniProt
Family T2R receptors (taste receptor GPCRs)	24	6	UniProt
Family fz/smo receptors	11	10	UniProt
Voltage-gated ion channels	132	99	IUPHAR-DB
Calcium-Activated Potassium Channels	7	7	IUPHAR-DB
CatSper and Two-Pore Channels	4	3	IUPHAR-DB
Cyclic Nucleotide-Regulated Channels	9	5	IUPHAR-DB
Inwardly Rectifying Potassium Channels	15	12	IUPHAR-DB
Transient Receptor Potential Channels	24	17	IUPHAR-DB
Two-P Potassium Channels	14	8	IUPHAR-DB
Voltage-Gated Calcium Channels	10	9	IUPHAR-DB
Voltage-Gated Potassium Channels	40	32	IUPHAR-DB
Voltage-Gated Sodium Channels	9	6	IUPHAR-DB
Predicted membrane proteins	5480	4462	MDM
Prediction method-based	5480	4462	MDM
Membrane proteins predicted by MDM	5480	4462	MDM
MEMSAT3 predicted membrane proteins *	7251	5948	MEMSAT3
MEMSAT-SVM predicted membrane proteins *	6302	5163	MEMSAT-SVM
Phobius predicted membrane proteins *	5770	4701	Phobius
SCAMPI predicted membrane proteins *	6365	5286	SCAMPI
SPOCTOPUS predicted membrane proteins *	7688	6477	SPOCTOPUS
THUMBUP predicted membrane proteins *	7151	5941	THUMBUP
TMHMM predicted membrane proteins *	5526	4438	TMHMM
GPCRHMM predicted membrane proteins *	806	430	GPCRHMM
# TM segments-based	5480	4462	MDM
1TM proteins predicted by MDM	3144	2741	MDM
9TM proteins predicted by MDM	135	118	MDM
8TM proteins predicted by MDM	160	138	MDM
7TM proteins predicted by MDM	937	551	MDM
6TM proteins predicted by MDM	311	269	MDM
5TM proteins predicted by MDM	289	238	MDM
4TM proteins predicted by MDM	551	467	MDM
3TM proteins predicted by MDM	579	500	MDM
2TM proteins predicted by MDM	948	834	MDM
>9TM proteins predicted by MDM	495	441	MDM
Predicted secreted proteins	2933	2491	HPA
Secreted proteins predicted by MDSEC	2933	2491	HPA
SignalP predicted secreted proteins *	2520	2121	SignalP
Phobius predicted secreted proteins *	3322	2843	Phobius
SPOCTOPUS predicted secreted proteins *	3690	3175	SPOCTOPUS
Predicted intracellular proteins	14895	13410	HPA
Plasma proteins	3739	3521	Plasma Proteome Database
Transcription factors	1497	1353	UMG
Yet undefined DNA-binding domains	19	18	UMG
Basic domains	173	154	UMG
Zinc-coordinating DNA-binding domains	778	711	UMG
Helix-turn-helix domains	393	347	UMG
Other all-alpha-helical DNA-binding domains	46	42	UMG
alpha-Helices exposed by beta-structures	13	13	UMG
Immunoglobulin fold	62	56	UMG
beta-Hairpin exposed by an alpha/beta-scaffold	14	13	UMG
beta-Sheet binding to DNA	5	5	UMG
beta-Barrel DNA-binding domains	3	3	UMG
RNA polymerase related proteins	29	28	KEGG
RAS pathway related proteins	229	204	KEGG
Citric acid cycle related proteins	30	29	KEGG
Disease and drug relatedⁱ The "Disease and drug related" table consists of a selection of gene lists related to diseases such as cancer and cardiovascular disease as well as genes associated with drug targets according to Drugbank.
Cancer-related genes	1713	1612
Candidate cancer biomarkers	1040	962	Plasma Proteome Institute
Mutated cancer genes	259	253	Publication
Mutational cancer driver genes	285	283	Publication
COSMIC somatic mutations in cancer genes	599	580	COSMIC
COSMIC Amplifications	18	16	COSMIC
COSMIC Splicing Mutations	75	74	COSMIC
COSMIC Somatic Mutations	558	542	COSMIC
COSMIC Other Mutations	37	37	COSMIC
COSMIC Nonsense Mutations	152	147	COSMIC
COSMIC Missense Mutations	242	235	COSMIC
COSMIC Large Deletions	40	40	COSMIC
COSMIC Germline Mutations	100	93	COSMIC
COSMIC Frameshift Mutations	150	144	COSMIC
COSMIC Translocations	345	334	COSMIC
Candidate cardiovascular disease genes	155	143	Plasma Proteome Institute
Disease related genes	3824	3513	UniProt
FDA approved drug targets	672	579	Drugbank
Biotech drugs	127	104	Drugbank
Small molecule drugs	576	496	Drugbank
Potential drug targets	1265	1173	HPA
Evidence basedⁱ For the "Evidence based" classes, further information can be found in the more detailed description of the protein evidence as well as on the protein evidence page.
Mapped to UniProt SWISS-PROT	18899	16649	UniProt
UniProt - Evidence at protein level	14731	13545	UniProt
UniProt - Evidence at transcript level	3522	2745	UniProt
UniProt - Inferred from homology	507	273	UniProt
UniProt - Predicted	94	61	UniProt
UniProt - Uncertain	67	44	UniProt
Protein evidence (Kim et al 2014)	12629	11887	Kim et al 2014
Protein evidence (Ezkurdia et al 2014)	11664	11163	Ezkurdia et al 2014

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg foundation.

Disease and drug relatediThe "Disease and drug related" table consists of a selection of gene lists related to diseases such as cancer and cardiovascular disease as well as genes associated with drug targets according to Drugbank.

Evidence basediFor the "Evidence based" classes, further information can be found in the more detailed description of the protein evidence as well as on the protein evidence page.

Disease and drug relatedⁱ
The "Disease and drug related" table consists of a selection of gene lists related to diseases such as cancer and cardiovascular disease as well as genes associated with drug targets according to Drugbank.

Evidence basedⁱ
For the "Evidence based" classes, further information can be found in the more detailed description of the protein evidence as well as on the protein evidence page.