SOX11 - Antibodies - The Human Protein Atlas


	Antibody HPA000448	Antibody HPA000536	Antibody CAB056152	Antibody CAB056153

ANTIBODY INFORMATION
Provider	Atlas Antibodies Sigma-Aldrich	Atlas Antibodies Sigma-Aldrich	Atlas Antibodies	Atlas Antibodies
Product name	HPA000448	HPA000536	AMAb90501	AMAb90502
Host species	Rabbit	Rabbit	Mouse	Mouse
Clonalityⁱ The antibodies are designated mAB for monoclonal and pAb for polyclonal.	pAb	pAb	mAb	mAb
Concentration	0.4 mg/ml	0.1303 mg/ml	Not known	Not known
Purity	Affinity purified using the PrEST-antigen as affinity ligand	Affinity purified using the PrEST-antigen as affinity ligand	Protein A/G	Protein A/G
Released in versionⁱ The release of the Human Protein Atlas in which the antibody was first published.	19.0	2.0	10.0	14.0
Referencesⁱ References to publications in which the antibody has been used.		23	1	1
Proper citation	n/a	Atlas Antibodies Cat#HPA000536, RRID:AB_1080060	Atlas Antibodies Cat#AMAb90501, RRID:AB_2665567	Atlas Antibodies Cat#AMAb90502, RRID:AB_2665568
Validation summaryⁱ All assays through which the antibody has been validated. Assays&annotation provide a detailed description of the different assays. The pie-charts indicate degree of validation.	ICC N/A IHC N/A WB PA	N/A ICC IHC N/A WB PA	N/A ICC IHC N/A WB N/A PA	N/A ICC IHC N/A WB N/A PA
IMMUNOCYTOCHEMISTRYⁱ Immunocytochemistry is used to validate the antibody staining and for assessing and validating the protein expression pattern in selected human cell lines.
Validationⁱ Results of validation by standard or enhanced validation. Standard validation is based on concordance with available experimental gene/protein characterization data in the UniProtKB/Swiss-Prot database. Standard validation results in scores Supported, Approved or Uncertain. Enhanced validation is performed using either siRNA knockdown, tagged GFP cell lines or independent antibodies. For the siRNA validation the decrease in antibody-based staining intensity upon target protein downregulation is evaluated. For the GFP validation the signal overlap between the antibody staining and the GFP-tagged protein is evaluated. For the independent antibodies validation the evaluation is based on comparison of the staining of two (or more) independent antibodies directed towards independent epitopes on the protein. For all cases except the siRNA validation, an image representative of the antibody staining pattern is shown. For the siRNA validation, a box plot of the results is shown.	Supportedⁱ Reliability scores for antibodies used in immunocytochemistry are set by comparing the staining pattern in cell lines with external experimental evidence for protein localization. The scores are termed Supported, Approved and Uncertain. The subcellular location is supported by literature. Immunofluorescent staining of human cell line SH-SY5Y shows localization to nucleoplasm.	N/A	N/A	N/A

Antibody dilution	Human assay: REH fixed with PFA, dilution: 1:200 Human assay: SH-SY5Y fixed with PFA, dilution: 1:200 Human assay: U2OS fixed with PFA, dilution: 1:200
IMMUNOHISTOCHEMISTRYⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain.
Validationⁱ Results of validation by standard or enhanced validation based on assessment of antibody performance in 44 normal tissues. Standard validation results in scores Supported, Approved or Uncertain. An image representative of the antibody staining pattern is shown. Enhanced validation results in the score Enhanced and includes two methods: Orthogonal validation and Independent antibody validation. For orthogonal validation, representative images of high and low expression are shown. For independent antibody validation, four images of each independent antibody are displayed.	N/A	Approvedⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain. Immunohistochemical staining of human caudate shows nuclear positivity in glial cells. Caudate	Approvedⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain. Immunohistochemical staining of human small intestine shows moderate nuclear positivity in subsets of cells. Small intestine	Approvedⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain. Immunohistochemical staining of human colon shows nuclear positivity in subsets of glandular cells. Colon

Retrievalⁱ Antigen retrieval is a method used to restore/retrieve the epitope (antibody bidning region) of the target protein, cross-linked, and thus masked, during tissue preserving fixative treatment of the tissues.		HIER pH6	HIER pH6	HIER pH6
Antibody dilution		1:100	1:500	1:500
Literature conformityⁱ Conformance of the expression pattern with available gene/protein characterization data in scientific literature and data from bioinformatic predictions. UniProt is used as the main source of gene/protein characterization data and when relevant, available publications and other sources of information are researched in depth. Extensive or sufficient gene/protein data requires that there is evidence of existence on a protein level and that a substantial quantity of published experimental data is available from literature and public databases. Limited protein/gene characterization data does not require evidence of existence on a protein level and refers to genes for which only bioinformatic predictions and scarce published experimental data is available.		Partly consistent with extensive gene/protein characterization data.	Partly consistent with extensive gene/protein characterization data.	Partly consistent with extensive gene/protein characterization data.
RNA consistencyⁱ Consistency between immunohistochemistry data and consensus RNA levels is divided into five different categories: i) High consistency, ii) Medium consistency, iii) Low consistency, iv) Very low consistency, and v) Cannot be evaluated.		Low consistency between antibody staining and RNA expression data.	Very low consistency between antibody staining and RNA expression data.	Low consistency between antibody staining and RNA expression data.
WESTERN BLOTⁱ A Western blot analysis is performed on a panel of human tissues and cell lines to evaluate antibody specificity. For antibodies with unreliable result a revalidation using an over-expression lysate is performed.
Validationⁱ Western Blot is used for quality control of the polyclonal antibodies generated in the project. After purification, the antibodies are used to detect bands in a setup of lysate and different tissues. The result is then scored Enhanced, Supported, Approved, or Uncertain. Enhanced validation includes five different methods: Genetic validation, Recombinant expression validation, Independent antibody validation, Orthogonal validation and Capture MS validation.	N/A	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.

Antibody dilution		1:500	1:1000	1:500
PROTEIN ARRAY
Validationⁱ A protein array containing 384 different antigens including the antibody target is used to analyse antibody specificity. Depending on the array interaction profile the antibody is scored as Supported, Approved, or Uncertain.	Approved Pass with quality comment low specificity (binding to 1-2 antigens >15% and <40%). Antibody specificity analysis with protein arrays. Predicted and matching interactions are shown in green.	Supported Pass with single peak corresponding to interaction only with its own antigen. Antibody specificity analysis with protein arrays. Predicted and matching interactions are shown in green.	N/A	N/A

Antibody dilution	1:1000	1:2000
RELEVANT PUBLICATIONS
		From gene expression analysis to tissue microarrays: a rational approach to identify therapeutic and diagnostic targets in lymphoid malignancies Ek S et al Mol Cell Proteomics 2006;5(6):1072-81	Assessment of SOX11 expression in routine lymphoma tissue sections: characterization of new monoclonal antibodies for diagnosis of mantle cell lymphoma Soldini D et al Am J Surg Pathol 2014;38(1):86-93	Assessment of SOX11 expression in routine lymphoma tissue sections: characterization of new monoclonal antibodies for diagnosis of mantle cell lymphoma Soldini D et al Am J Surg Pathol 2014;38(1):86-93
		Nuclear expression of the non B-cell lineage Sox11 transcription factor identifies mantle cell lymphoma Ek S et al Blood 2008;111(2):800-5
		The subcellular Sox11 distribution pattern identifies subsets of mantle cell lymphoma: correlation to overall survival Wang X et al Br J Haematol 2008;143(2):248-52
		Nuclear expression of sox11 is highly associated with mantle cell lymphoma but is independent of t(11;14)(q13;q32) in non-mantle cell B-cell neoplasms Chen YH et al Mod Pathol 2010;23(1):105-12
		SOX11 expression is highly specific for mantle cell lymphoma and identifies the cyclin D1-negative subtype Mozos A et al Haematologica 2009;94(11):1555-62
		Strong lymphoid nuclear expression of SOX11 transcription factor defines lymphoblastic neoplasms, mantle cell lymphoma and Burkitt's lymphoma Dictor M et al Haematologica 2009;94(11):1563-8
		Genomic and gene expression profiling defines indolent forms of mantle cell lymphoma Fernàndez V et al Cancer Res 2010;70(4):1408-18
		Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network Aiden AP et al Cell Stem Cell 2010;6(6):591-602
		SOX11 expression correlates to promoter methylation and regulates tumor growth in hematopoietic malignancies Gustavsson E et al Mol Cancer 2010;9:187
		Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma Wang X et al PLoS One 2010;5(11):e14085
		The expression of SOX11, cyclin D1, cyclin D2, and cyclin D3 in B-cell lymphocytic proliferative diseases Cao X et al Med Oncol 2012;29(2):1190-6
		Indolent mantle cell leukemia: a clinicopathological variant characterized by isolated lymphocytosis, interstitial bone marrow involvement, kappa light chain restriction, and good prognosis Ondrejka SL et al Haematologica 2011;96(8):1121-7
		Small cell variant of mantle cell lymphoma is an indolent lymphoma characterized by bone marrow involvement, splenomegaly, and a low Ki-67 index Kimura Y et al Cancer Sci 2011;102(9):1734-41
		The tumour suppressor SOX11 is associated with improved survival among high grade epithelial ovarian cancers and is regulated by reversible promoter methylation Sernbo S et al BMC Cancer 2011;11:405
		In situ mantle cell lymphoma: clinical implications of an incidental finding with indolent clinical behavior Carvajal-Cuenca A et al Haematologica 2012;97(2):270-8
		Prognostic role of SOX11 in a population-based cohort of mantle cell lymphoma Nygren L et al Blood 2012;119(18):4215-23
		High-resolution chromatin immunoprecipitation (ChIP) sequencing reveals novel binding targets and prognostic role for SOX11 in mantle cell lymphoma Kuo PY et al Oncogene 2015;34(10):1231-40 Application: ChIP, IHC, WB
		The clinical role of epithelial-mesenchymal transition and stem cell markers in advanced-stage ovarian serous carcinoma effusions Davidson B et al Hum Pathol 2015;46(1):1-8 Application: IHC
		Tripeptidyl Peptidase II Mediates Levels of Nuclear Phosphorylated ERK1 and ERK2 Wiemhoefer A et al Mol Cell Proteomics 2015;14(8):2177-93 Application: WB
		Persistence of a t(11;14)-positive clone in a patient with mantle cell lymphoma for 20 years Otsuka Y et al Clin Case Rep 2017;5(4):477-481 Application: IHC
		Impact of over-expression in Ba/F3 cells Lord M et al Haematologica 2018;103(12):e594-e597 Application: WB
		SOX11: friend or foe in tumor prevention and carcinogenesis? Yang Z et al Ther Adv Med Oncol 2019;11:1758835919853449
		Diagnostic accuracy of SOX11 immunohistochemistry in mantle cell lymphoma: A meta-analysis Lee W et al PLoS One 2019;14(11):e0225096 Application: IHC
ANTIGEN INFORMATION
Antigen	Recombinant protein fragment	Recombinant protein fragment	Recombinant protein	Recombinant protein
Length (aa)	117	111
Antigen sequence	`EDDDDDELQLQIKQEPDEEDEEPPHQQLLQPPGQQPSQLLRRYNVAKVPA SPTLSSSAESPEGASLYDEVRAGATSGAGGGSRLYYSFKNITKQHPPPLA QPALSPASSRSVSTSSS`	`FMVWSKIERRKIMEQSPDMHNAEISKRLGKRWKMLKDSEKIPFIREAERL RLKHMADYPDYKYRPRKKPKMDPSAKPSASQSPEKSAAGGGGGSAGGGAG GAKTSKGSSKK`
Matching transcripts	SOX11-201 - ENSP00000322568 [99%]	SOX11-201 - ENSP00000322568 [100%]
Matching mouse transcripts	ENSMUSP00000078070 [73%] ENSMUSP00000137645 [26%]	ENSMUSP00000078070 [82%] ENSMUSP00000100013 [69%] ENSMUSP00000064250 [63%]
ANTIGEN VIEWⁱ The Structure section provides in-house generated structures, predicted using the Alphafold source code, for the majority of the proteins and their related isoforms. Displaying protein features on the AlphaFold structures Individual splice variants can be selected in the top part of the Protein Browser (see below) and different transcript-related features such as transmembrane regions, InterPro domains and antigen sequences for antibodies can be displayed in the structure by clicking on the respective features in the Protein Browser. Clinical and population-based amino acid variants based on data from the Ensembl variation database and AlphaMissense (AM) predictions can be highlighted using the sliders to the right of the structure. These can also be used to colour the entire structure by residue index or make the structure autorotate.The structures are displayed using the NGL Viewer and can also be zoomed-in and rotated manually. The Protein Browser The ProteinBrowser displays the antigen location on the target protein(s) and the features of the target protein. Transcript names and schematic transcript structures including exons, introns and UTRs for the different isoforms are shown on top, and can be used to switch between the structures for the different splice variants. 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. Below 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). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more). The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more). Signal peptides (turquoise) and membrane regions (orange) based on predictions using the majority decision methods MDM and MDSEC are also 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.

SOX11-201

Displaying protein features on the AlphaFold structures

The Protein Browser