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Field

Term
Gene name

Class

Subclass

Chromosome

External id

In atlas

Reliability

Reliability

Reliability

Validation

Method

Validation

Method

Validation

Method

Validation

Location

Searches

Tissue

Cell type

Expression

Tissue

Specificity

Cell line

Specificity

Cancer

Specificity

Tissue

Detectable

Cell line

Detectable

Cancer

Detectable

Cancer

Prognosis

Category

Score

Score

Score

Antibodies

Column

 
 
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SRF
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PATHOLOGY ATLAS

GENE/PROTEIN

Antibody validation

Dictionary

Level of antibody staining/expression





High
Medium
Low
Not detected

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

SRF

Gene descriptioni

Gene description according to HGNC.

Serum response factor

Protein classi

Protein class the gene product belongs to according to selected gene lists. List of protein classes.

Predicted intracellular proteins
Transcription factors

Predicted localizationi

Protein localization predicted from several bioinformatic algorithms.

Read more

Intracellular

Number of transcriptsi

Number of protein-coding transcribed from this gene as defined by Ensembl.

1
SHOW MORE

HUMAN PROTEIN ATLAS INFORMATION

RNA categoryi

RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.

TCGA (cancer tissue):Expressed in all
HPA (cell line):Expressed in all
HPA (normal tissue):Expressed in all

Protein evidencei

Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.

Evidence at protein level

Protein expression
normal tissuei

A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.

"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.

Read more

General nuclear expression.

ANTIBODY IHC RELIABILITY

Data reliability
descriptioni

Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.

Antibody staining mainly consistent with RNA expression data.

Reliability scorei

Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.

Read more

Supported based on 2 antibodies.
HPA001819 , CAB005416
SHOW MORE

PROGNOSTIC SUMMARYi

Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.

Prognostic marker in renal cancer (unfavourable).
Renal cancer p<0.001
Show all

RNA EXPRESSION OVERVIEWi

RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).

TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name.

Read more
RNA cancer category: Expressed in all

PROTEIN EXPRESSIONi

Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.

For histological reference, visit the histological dictionary.

Colorectal cancer
Breast cancer
Prostate cancer
Lung cancer
Lymphoma

STAINING SUMMARYi

For each cancer, the fraction of samples with protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the left). The length of the bar represents the number of patient samples analyzed (max=12 patients). The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies. The mouse-over function displays additional data for the features in the staining summary view.

Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.

HPA001819
CAB005416

Cancer

Cancer staining

Protein
expression of
normal tissue

Breast cancer
 
Carcinoid
 
Cervical cancer
 
 
Colorectal cancer
 
 
Endometrial cancer
 
 
Glioma
 
Head and neck cancer
 
 
Liver cancer
 
 
Lung cancer
 
 
Lymphoma
 
 
 

Cancer

Cancer staining

Protein
expression of
normal tissue

Melanoma
 
Ovarian cancer
 
Pancreatic cancer
 
Prostate cancer
 
Renal cancer
 
Skin cancer
 
Stomach cancer
 
 
Testis cancer
 
Thyroid cancer
 
Urothelial cancer
 

Staining summaryi

A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.

A majority of malignant tissues showed weak to moderate nuclear immunoreactivity. Stomach- and pancreatic cancers and most malignant gliomas and endometrial cancers were negative.

Cancer

Cancer staining

Protein
expression of
normal tissue

Breast cancer
 
Carcinoid
 
Cervical cancer
 
 
Colorectal cancer
 
 
Endometrial cancer
 
 
Glioma
 
Head and neck cancer
 
 
Liver cancer
 
 
Lung cancer
 
 
Lymphoma
 
 
 

Cancer

Cancer staining

Protein
expression of
normal tissue

Melanoma
 
Ovarian cancer
 
Pancreatic cancer
 
Prostate cancer
 
Renal cancer
 
Skin cancer
 
Stomach cancer
 
 
Testis cancer
 
Thyroid cancer
 
Urothelial cancer
 

Staining summaryi

A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.

Malignant cells showed weak to moderate nuclear immunoreactivity. Additional cytoplasmic positivity was observed in a several cases.

GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Gene name

SRF (HGNC Symbol)

Synonyms

MCM1

Description

Serum response factor (HGNC Symbol)

Entrez gene summary

This gene encodes a ubiquitous nuclear protein that stimulates both cell proliferation and differentiation. It is a member of the MADS (MCM1, Agamous, Deficiens, and SRF) box superfamily of transcription factors. This protein binds to the serum response element (SRE) in the promoter region of target genes. This protein regulates the activity of many immediate-early genes, for example c-fos, and thereby participates in cell cycle regulation, apoptosis, cell growth, and cell differentiation. This gene is the downstream target of many pathways; for example, the mitogen-activated protein kinase pathway (MAPK) that acts through the ternary complex factors (TCFs). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

Chromosome

6

Cytoband

p21.1

Chromosome location (bp)

43171299 - 43181507

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000112658 (version 83.38)

Entrez gene

6722

UniProt

P11831 (UniProt - Evidence at protein level)

neXtProt

NX_P11831

Antibodypedia

SRF antibodies

PROTEIN BROWSERi

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50) (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.

SRF-001

PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.

Splice variant

UniProt

Protein class

Gene ontology

Length & mass

Signal peptide
(predicted)

Transmembrane regions
(predicted)

SRF-001
ENSP00000265354
ENST00000265354
P11831 [Direct mapping]
Serum response factor
A0A024RD16 [Target identity:100%; Query identity:100%]
Serum response factor (C-fos serum response element-binding transcription factor), isoform CRA_a
Show all
   SPOCTOPUS predicted secreted proteins
Predicted intracellular proteins
Transcription factors
   alpha-Helices exposed by beta-structures
Protein evidence (Kim et al 2014)
Show all
GO:0000790 [nuclear chromatin]
GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding]
GO:0000983 [transcription factor activity, RNA polymerase II core promoter sequence-specific]
GO:0001076 [transcription factor activity, RNA polymerase II transcription factor binding]
GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding]
GO:0001228 [transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding]
GO:0001569 [patterning of blood vessels]
GO:0001666 [response to hypoxia]
GO:0001701 [in utero embryonic development]
GO:0001707 [mesoderm formation]
GO:0001764 [neuron migration]
GO:0001829 [trophectodermal cell differentiation]
GO:0001947 [heart looping]
GO:0002011 [morphogenesis of an epithelial sheet]
GO:0002042 [cell migration involved in sprouting angiogenesis]
GO:0002521 [leukocyte differentiation]
GO:0003257 [positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation]
GO:0003677 [DNA binding]
GO:0003682 [chromatin binding]
GO:0003700 [transcription factor activity, sequence-specific DNA binding]
GO:0003705 [transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding]
GO:0005515 [protein binding]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0006355 [regulation of transcription, DNA-templated]
GO:0006366 [transcription from RNA polymerase II promoter]
GO:0007015 [actin filament organization]
GO:0007160 [cell-matrix adhesion]
GO:0007264 [small GTPase mediated signal transduction]
GO:0007369 [gastrulation]
GO:0007507 [heart development]
GO:0007616 [long-term memory]
GO:0008134 [transcription factor binding]
GO:0008285 [negative regulation of cell proliferation]
GO:0008306 [associative learning]
GO:0009636 [response to toxic substance]
GO:0009725 [response to hormone]
GO:0010669 [epithelial structure maintenance]
GO:0010735 [positive regulation of transcription via serum response element binding]
GO:0010736 [serum response element binding]
GO:0016337 [single organismal cell-cell adhesion]
GO:0021766 [hippocampus development]
GO:0022028 [tangential migration from the subventricular zone to the olfactory bulb]
GO:0030036 [actin cytoskeleton organization]
GO:0030038 [contractile actin filament bundle assembly]
GO:0030155 [regulation of cell adhesion]
GO:0030168 [platelet activation]
GO:0030220 [platelet formation]
GO:0030336 [negative regulation of cell migration]
GO:0030878 [thyroid gland development]
GO:0031175 [neuron projection development]
GO:0031490 [chromatin DNA binding]
GO:0033561 [regulation of water loss via skin]
GO:0034097 [response to cytokine]
GO:0035855 [megakaryocyte development]
GO:0035912 [dorsal aorta morphogenesis]
GO:0042789 [mRNA transcription from RNA polymerase II promoter]
GO:0042803 [protein homodimerization activity]
GO:0042826 [histone deacetylase binding]
GO:0043149 [stress fiber assembly]
GO:0043565 [sequence-specific DNA binding]
GO:0043589 [skin morphogenesis]
GO:0045059 [positive thymic T cell selection]
GO:0045214 [sarcomere organization]
GO:0045597 [positive regulation of cell differentiation]
GO:0045773 [positive regulation of axon extension]
GO:0045893 [positive regulation of transcription, DNA-templated]
GO:0045944 [positive regulation of transcription from RNA polymerase II promoter]
GO:0045987 [positive regulation of smooth muscle contraction]
GO:0046016 [positive regulation of transcription by glucose]
GO:0046716 [muscle cell cellular homeostasis]
GO:0046983 [protein dimerization activity]
GO:0048538 [thymus development]
GO:0048589 [developmental growth]
GO:0048666 [neuron development]
GO:0048821 [erythrocyte development]
GO:0051091 [positive regulation of sequence-specific DNA binding transcription factor activity]
GO:0051150 [regulation of smooth muscle cell differentiation]
GO:0051491 [positive regulation of filopodium assembly]
GO:0055003 [cardiac myofibril assembly]
GO:0060055 [angiogenesis involved in wound healing]
GO:0060218 [hematopoietic stem cell differentiation]
GO:0060261 [positive regulation of transcription initiation from RNA polymerase II promoter]
GO:0060292 [long term synaptic depression]
GO:0060324 [face development]
GO:0060347 [heart trabecula formation]
GO:0060425 [lung morphogenesis]
GO:0060532 [bronchus cartilage development]
GO:0060534 [trachea cartilage development]
GO:0060947 [cardiac vascular smooth muscle cell differentiation]
GO:0061029 [eyelid development in camera-type eye]
GO:0061145 [lung smooth muscle development]
GO:0070830 [bicellular tight junction assembly]
GO:0070878 [primary miRNA binding]
GO:0071333 [cellular response to glucose stimulus]
GO:0090009 [primitive streak formation]
GO:0090136 [epithelial cell-cell adhesion]
GO:0090398 [cellular senescence]
GO:1900222 [negative regulation of beta-amyloid clearance]
GO:1902894 [negative regulation of pri-miRNA transcription from RNA polymerase II promoter]
GO:1902895 [positive regulation of pri-miRNA transcription from RNA polymerase II promoter]
Show all
508 aa
51.6 kDa
No 0

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The Human Protein Atlas project is funded
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