YES1 / Tyrosine-protein kinase Yes · IHC design guide

Design Immunohistochemistry for YES1

Plan YES1 staining in paraffin sections using the widespread cytoplasmic pattern reported in tissue IHC (HPA tissue IHC). The guide covers controls and interpretation using the catalog antibody at 0.5–1 μg/ml (datasheet: PB9466).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for YES1 (IHC for YES1): expected localisation Cytoplasmic staining (HPA tissue IHC), antibody PB9466, validated IHC image, and IHC protocol steps — Printable **YES1** IHC protocol sheet — expected localisation Cytoplasmic staining (HPA tissue IHC), antibody PB9466, controls and protocol steps. Open the full YES1 IHC guide →

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YES1 Immunohistochemistry Experimental Design Guide

Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.

Must know before staining

	Expected localisation	Cytoplasmic staining (HPA tissue IHC)
	Staining pattern	Widespread cytoplasmic staining (HPA tissue IHC)
	Antigen retrieval	EDTA pH 8.0 HIER, heat-mediated (datasheet PB9466)
	Positive control ⓘ	Adipose tissue+4 more · see all
	Negative control ⓘ	Spleen

Important caveats

Reasons your staining may differ from the expected pattern.

	Fixation	Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific)
	Caveat	Antibody staining has low consistency with RNA data (HPA tissue IHC)
	Regulation	Broad expression; inducer unknown (HPA tissue IHC; UniProt)
	Isoform / epitope	No listed isoforms or transmembrane segment (UniProt)

Section 1

Recommended YES1 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet: PB9466) is accompanied by published YES1 staining protocols for mouse tumor sections (PMC5561618) and tissue microarrays (PMC7931761).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded human mammary cancer tissue; fixative not specified (datasheet PB9466)
Fixation	Image fixative and duration unreported (datasheet PB9466); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat retrieval: EDTA pH 8.0 (datasheet PB9466); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet PB9466)
Primary antibody	Rabbit anti-YES1, 0.5-1μg/ml (datasheet PB9466)
Primary incubation	Overnight at 4 °C (datasheet PB9466)
Detection	Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9466)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	YES1-positive staining in adipocytes of adipose tissue (HPA tissue IHC: Medium). HPA tissue profile: Ubiquitous cytoplasmic expression. No signal in the no-primary control.

💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet: PB9466); consider citrate at pH 6.0 when adapting either published protocol (PMC5561618; PMC7931761).

Section 2

What Is the Expected YES1 Staining Pattern?

YES1 is a nontransmembrane kinase found in cytosol, at the cell membrane and at cell junctions (UniProt P07947: topology and subcellular location). In tissue IHC, expect predominantly cytoplasmic staining across many cell types, including adipocytes and respiratory epithelial cells (HPA: ubiquitous cytoplasmic expression; Medium in both). Interpret intensity cautiously: the HPA IHC profile is Approved but has low consistency with RNA expression (HPA: reliability description).

What am I looking at on my slide?
Cytoplasmic chromogen in adipocytes or bronchial respiratory epithelium, around Medium intensity.	This matches observed YES1 staining in those cells (HPA: Medium in adipocytes and bronchial respiratory epithelial cells). Membrane enrichment can be plausible given YES1 localisation (UniProt P07947: cell membrane), but HPA tissue IHC describes a broadly cytoplasmic pattern; a crisp membrane rim is not required for a positive call (HPA: tissue profile).
Strong, predominantly nuclear staining with little cytoplasmic signal.	A nuclear-only pattern conflicts with the supplied localisation evidence (UniProt P07947: cytosol, membrane and junction; HPA ICC-IF: supported plasma membrane and cytosol). Treat it as a possible artefact. Review the negative control and staining distribution, then reassess antibody specificity before assigning the signal to YES1 (general IHC practice).
Prominent signal in splenic red-pulp cells despite a clean positive-tissue control.	HPA reports YES1 as Not detected in red-pulp cells (HPA: spleen IHC). Investigate cross-reactivity or endogenous chromogenic activity, especially if the signal persists in a no-primary control (general IHC practice). This is a caution, not proof of an absent target: HPA notes low staining–RNA consistency, and UniProt describes fetal splenic hematopoietic expression (HPA: reliability description; UniProt P07947: tissue specificity).
Uniform haze across tissue, blank areas or several unrelated cell types.	A widespread haze that ignores tissue boundaries is hard to reconcile with a cell-associated cytoplasmic pattern (HPA: tissue profile). Check the no-primary control for endogenous detection activity; review blocking, washing and antibody concentration if the haze requires primary antibody (general IHC practice). Broad YES1 staining alone is not abnormal, because HPA describes ubiquitous expression (HPA: tissue profile).
No signal in adipocytes and bronchial respiratory epithelium processed alongside the study sample.	Both are observed at Medium intensity in HPA tissue IHC (HPA: adipose tissue and bronchus). If both controls fail, first investigate the run: section integrity, retrieval conditions, antibody dilution and chromogen development (general IHC practice). A blank study sample cannot be interpreted confidently until a known-positive control stains; HPA's Approved rating does not guarantee every run (HPA: IHC reliability).

💡Expected YES1 appearanceCall a positive result when cell-associated, mainly cytoplasmic chromogen is visible in an HPA-observed cell type such as adipocytes or bronchial respiratory epithelium at roughly Medium intensity; isolated nuclear staining or control-positive diffuse haze is suspect (HPA: tissue IHC profile and Medium levels; UniProt P07947: subcellular location; general IHC practice).

How each factor affects the staining
Compartment and topology	YES1 has no transmembrane segment, yet localises to the cell membrane, cytosol and cell junctions (UniProt P07947: topology and subcellular location). Evaluate membrane-associated staining in the context of the dominant cytoplasmic tissue pattern; absence of a sharp membrane outline does not by itself invalidate IHC (HPA: tissue profile).
Tissue reference and confidence	HPA calls tissue staining ubiquitous and cytoplasmic, with low RNA tissue specificity (HPA: tissue profile; RNA specificity). Its IHC reliability is Approved, with low consistency between staining and RNA expression (HPA: reliability description). Use the listed cell-level observations as practical references, not an absolute expression map.
Antibody validation	HPA026480 and CAB004370 each have Approved IHC status; HPA026480 also has Supported ICC status (HPA: antibody validation). These labels apply to the listed antibodies and applications. They do not validate an unlisted antibody, establish an IHC dilution or upgrade the tissue profile to an Enhanced rating.
Processing and target forms	UniProt lists one chain spanning residues 2–543, no signal peptide or propeptide, no annotated glycosylation sites and no isoforms in this payload (UniProt P07947: processing, glycosylation and isoforms). Those entries provide no basis for predicting tissue shedding, an isoform-specific stain or a retrieval condition.
IF/ICC Q: What localisation should be expected?	A: Plasma-membrane and cytosolic fluorescence is supported in the HPA ICC-IF record (HPA: supported main locations). That record lists images from A-431, U-251MG, U2OS, RPTEC/TERT1 and serum-starved hTERT-RPE1 (HPA: ICC-IF image lines). This answers localisation only; IF/ICC workflow belongs in its own guide.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Positive tissue and study sections are both blank.	A shared staining-run failure is possible; HPA reports Medium staining in adipocytes and bronchial respiratory epithelium (HPA: tissue IHC).	Check section integrity, retrieval, primary dilution, detection reagents and chromogen with a known-positive section (general IHC practice). Reassess the study sample only after that control works.
Signal is nuclear while cytoplasm is clear.	The pattern conflicts with supplied YES1 localisation (UniProt P07947: subcellular location; HPA: supported ICC-IF locations).	Inspect no-primary and positive controls, confirm staining is cell-associated, and compare a separately validated IHC antibody if available (general IHC practice; HPA: two Approved IHC antibodies).
Brown signal appears in splenic red pulp.	HPA lists these cells as Not detected; endogenous enzyme activity or antibody cross-reactivity could account for unexpected chromogen (HPA: spleen IHC; general IHC practice).	Run a no-primary control and appropriate endogenous-enzyme blocking control, then compare the cell-level pattern with a known-positive tissue (general IHC practice). Do not use spleen as an absolute negative reference across ages (UniProt P07947: fetal spleen expression).
All tissue compartments look equally hazy.	Background from detection, insufficient washing or excess antibody is possible (general IHC practice); broad YES1 expression can also produce genuine cell-associated signal (HPA: ubiquitous cytoplasmic profile).	Compare tissue-free areas and no-primary controls; adjust blocking, washing or primary concentration only when controls identify background (general IHC practice). Preserve discrete cytoplasmic staining during optimisation.
Only a weak signal appears in oral mucosa, liver or esophagus.	HPA records Low staining in squamous oral or esophageal epithelium and in hepatocytes (HPA: low tissue-IHC observations).	Judge these slides beside a Medium reference such as bronchial respiratory epithelium, and verify control performance before increasing signal amplification (HPA: bronchus Medium; general IHC practice).
A sharp membrane rim is absent, but cytoplasmic signal is present.	Membrane localisation is supported, while HPA's tissue IHC summary emphasises cytoplasmic staining (UniProt P07947: cell membrane; HPA: tissue profile).	Score the cell-associated cytoplasmic signal against an HPA-observed positive cell type and its control; avoid rejecting a section solely for lacking a continuous membrane rim (HPA: tissue IHC profile; general IHC practice).

Source: UniProt P07947 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing YES1 staining

IHC analysis of YES1 using anti-YES1 antibody (PB9466). YES1 was detected in a paraffin-embedded section of human mammary cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1 μg/ml rabbit anti-YES1 Antibody (PB9466) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.

PB9466 · IHCIHC analysis of YES1 using anti-YES1 antibody (PB9466). YES1 was detected in a paraffin-embedded section of human mammary cancer tissue. Hea

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000176105-YES1/tissue/cerebral+cortex#imid_6551432

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000176105-YES1/tissue/colon#imid_6551366

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000176105-YES1/tissue/liver#imid_6551351

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000176105-YES1/tissue/kidney#imid_6551360

HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA026480; green = YES1, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for YES1 IHC & IF

🧪Run bronchus first and require staining in respiratory epithelial cells (HPA: Medium in bronchus respiratory epithelial cells); use spleen red-pulp cells as the negative tissue comparator (HPA: Not detected in spleen red-pulp cells). On the bronchus slide, use adjacent cells as internal negative comparators only if they show counterstain without specific DAB signal; verify this on the slide because the supplied HPA row identifies respiratory epithelial cells, not negative cell types (HPA: Medium in bronchus respiratory epithelial cells).

Positive control tissue: Adipose tissue (Adipocytes, HPA Medium)

Negative control tissue: Spleen (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show YES1 in A-431, U-251MG, U2OS, RPTEC/TERT1, hTERT-RPE1 (serum starved), with annotated localisation: Plasma membrane (supported), Cytosol (supported) (HPA subcellular).

Technical controls: Include a no-primary secondary-only control, a host-matched rabbit IgG control matched to the primary’s clonality where known, and a YES1-knockout specimen or validated peptide-block control (caption: rabbit anti-YES1 antibody; standard IHC practice). Block endogenous peroxidase and check endogenous biotin background when using the caption’s biotinylated secondary, streptavidin-biotin detection and DAB (caption: biotinylated goat anti-rabbit IgG, SABC and DAB).

⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PB9466 paraffin-section caption does not state a fixative (caption: fixative unreported). Start retrieval optimization with heat-mediated EDTA at pH 8.0, as used in the supplied IHC caption (caption: EDTA pH 8.0); the supplied evidence does not establish whether frozen-section IHC or IF is easier, although ICC-IF images are available (HPA: YES1 subcellular ICC-IF images). In bronchus, check mucus-associated background against the negative controls before scoring epithelial DAB signal (standard IHC practice; HPA: Medium in bronchus respiratory epithelial cells).

HPA tissue IHC evidence for YES1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	Medium	Protein (IHC)	HPA →
Adrenal gland	Glandular cells	Medium	Protein (IHC)	HPA →
Appendix	Glandular cells	Medium	Protein (IHC)	HPA →
Breast	Adipocytes	Medium	Protein (IHC)	HPA →
Bronchus	Respiratory epithelial cells	Medium	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Spleen	Cells in red pulp	Not detected	Protein (IHC)	HPA →

Section 3

Advanced YES1 IHC Tips

Troubleshoot YES1 chromogenic IHC in paraffin sections by checking retrieval, staining compartment, controls, and scoring against the supplied tissue evidence.

How should I retrieve YES1 antigen when staining paraffin sections?

Start with heat-mediated retrieval in EDTA at pH 8.0 for PB9466 paraffin-section IHC (datasheet PB9466). The documented example then used 10% goat serum block, 1 μg/ml primary antibody overnight at 4°C, and a biotinylated secondary for 30 minutes at 37°C (datasheet PB9466). If staining is weak, compare retrieval duration on serial sections while holding antibody concentration and detection conditions constant, and check that tissue morphology remains intact (standard IHC practice). Record heating, cooling, and wash conditions for each run so a change in staining can be traced to retrieval rather than detection (standard IHC practice).

Could fixation explain weak or uneven YES1 staining?

The PB9466 tissue example identifies a paraffin-embedded section but does not state its fixative, so target-specific fixation sensitivity is unknown (datasheet PB9466). Record the specimen’s actual fixative and fixation interval, then compare similarly processed sections before changing retrieval or antibody concentration (standard IHC practice). If signal varies across a section, examine morphology and staining at the cut edge alongside the central tissue; processing gradients can create misleading spatial differences (standard IHC practice). Use a consistently processed positive control in each run and interpret any improvement after a processing change as a workflow result, not proof of a YES1-specific fixation effect (standard IHC practice).

Which YES1 staining compartments should I expect in tissue?

Expect predominantly cytoplasmic staining in the HPA tissue IHC profile, while considering membrane-associated signal when its cell boundaries are convincing (HPA: ubiquitous cytoplasmic expression; HPA subcellular: supported plasma membrane and cytosol). YES1 is also annotated at cell junctions and the centrosome, with newly synthesized protein accumulating initially near the Golgi (UniProt P07947 subcellular). Because YES1 has no transmembrane segment, a membrane pattern should not be interpreted as a transmembrane protein signal (UniProt P07947 topology). Compare the pattern with intact cell morphology and a matched negative control; isolated nuclear or diffuse extracellular color warrants investigation before it is scored as YES1 (standard IHC practice; UniProt P07947 subcellular).

Could epitope choice change the apparent YES1 pattern?

The supplied record lists no alternate YES1 isoforms, and the PB9466 tissue caption does not identify the antibody epitope; neither establishes which sequence or state the antibody recognizes (UniProt P07947 isoforms; datasheet PB9466). YES1 contains SH3 at residues 91–152, SH2 at 158–255, and kinase domain at 277–530, with reported modified residues including phosphotyrosines 336 and 345 (UniProt P07947 domains; UniProt P07947 modified residues). Check the supplier’s epitope information before attributing discordant staining to a domain or phosphorylation state (standard IHC practice). If specificity is uncertain, compare independent antibody epitopes and appropriate loss-of-target controls under matched section-processing conditions (standard IHC practice).

How can IF help resolve an ambiguous YES1 IHC pattern?

Use IF as an orthogonal localisation check, pairing YES1 with a marker for the cell type being assessed, such as a renal proximal-tubule epithelial marker when examining renal tissue (UniProt P07947 tissue specificity; standard IF practice). Choose spectrally separated fluorophores and inspect unstained tissue in each channel so autofluorescence is distinguishable from specific signal (standard IF practice). YES1 lacks a transmembrane segment and has supported cytosolic and plasma-membrane localisation, but the antibody’s epitope side is unspecified (UniProt P07947 topology; HPA subcellular; datasheet PB9466). For an intracellular epitope, compare permeabilised and non-permeabilised preparations and assess whether membrane and cytosolic patterns remain anatomically plausible (standard IF practice; HPA subcellular).

How do I reduce diffuse or cell-specific background?

Begin with the documented 10% goat serum block and 1 μg/ml PB9466 primary concentration, then adjust one condition at a time if background persists (datasheet PB9466; standard IHC practice). Because the documented detection uses a biotinylated secondary, a streptavidin–biotin complex, and DAB, check secondary-only and detection-only controls for signal unrelated to primary binding (datasheet PB9466; standard IHC practice). Include a peroxidase block before DAB development and assess whether endogenous tissue activity or precipitate follows the apparent positive cells (standard IHC practice). Compare background with intact morphology and adjacent sections before treating diffuse color as the widespread cytoplasmic YES1 pattern reported by HPA (HPA: ubiquitous cytoplasmic expression; standard IHC practice).

What is a defensible way to score YES1 IHC? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and compartment before scoring, because HPA reports widespread cytoplasmic staining while YES1 also has supported membrane localisation (HPA tissue IHC; HPA subcellular). For a defined cell population, report percent positive cells and an intensity-weighted H-score from 0–300, with cytoplasmic and membrane results recorded separately when both are evaluable (standard IHC practice). For spatial analyses, report positive-cell density per mm² of viable tissue and normalise counts to the corresponding viable area, excluding folds and necrosis (standard IHC practice). Hold retrieval, DAB development, imaging, and scoring thresholds constant across specimens, and document the control section used to set background (standard IHC practice).

When is YES1 staining convincing rather than artefactual?

A convincing result follows intact cells and a plausible cytoplasmic or cell-boundary pattern, consistent with the HPA tissue and subcellular observations (HPA tissue IHC; HPA subcellular). In adult tissue, renal proximal-tubule epithelium and basal epidermal keratinocytes are documented YES1-expressing populations, but their presence alone does not validate an antibody signal (UniProt P07947 tissue specificity; standard IHC practice). Be cautious with staining confined to cut edges, necrotic regions, extracellular deposits, or compartments unsupported by the localisation record, and check detection-only controls for endogenous enzyme activity (standard IHC practice; UniProt P07947 subcellular). HPA rates its tissue staining approved while reporting low consistency with RNA expression, so resolve consequential discrepancies with independent evidence (HPA: reliability description; standard IHC practice).

Boster reagents

Best YES1 / Tyrosine-protein kinase Yes IHC Antibodies

The catalog lists human-reactive YES1 antibodies for IHC and IF/ICC (catalog applications/reactivity). The supplied image documents IHC in a human mammary cancer paraffin section (PB9466 IHC caption).

Real IHC data

Anti-Yes1 Antibody ®

Cat # PB9466

View product →

PB9466 is the sole rendering card, with IHC shown in a paraffin-embedded human mammary cancer section (cards payload; PB9466 IHC caption). It is listed for human IHC at 0.5–1 μg/ml; no IF image is supplied (catalog applications/reactivity/IHC dilution/IF image alts).

Which to pick: For human tissue IHC, choose PB9466: its own image documents a paraffin section with EDTA pH 8.0 retrieval and DAB detection; the fixative is unreported (PB9466 IHC caption). For IF/ICC, choose M02640-2 because those applications are listed for it, though no IF image is supplied (catalog applications/IF image alts). For mouse or rat samples, M02640-2 is the listed cross-species option: it is a rabbit monoclonal, clone 19Y44, with human, mouse and rat reactivity (catalog host/clone/reactivity).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

UniProt Consortium. UniProt entry P07947 (YES_HUMAN, Tyrosine-protein kinase Yes).
Human Protein Atlas. YES1 tissue IHC expression (reliability: Approved).
Human Protein Atlas. YES1 subcellular location (ICC-IF): Localized to the plasma membrane and cytosol..
Human Protein Atlas. YES1 antibody validation summary (2 antibodies).
YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics. Proceedings of the National Academy of Sciences of the United States of America 2018 — PMC6042104.
Candidate Biomarkers YES1, Troponin I, Lactate, and Ammonia for Evaluation of Cardiac Function Post Hypothermic Oxygenated Perfusion. ASAIO journal (American Society for Artificial Internal Organs : 1992) 2025 — PMC12462677.
miR-140-5p suppresses the proliferation, migration and invasion of gastric cancer by regulating YES1. Molecular cancer 2017 — PMC5561618.
SRC family kinase (SFK) inhibitor dasatinib improves the antitumor activity of anti-PD-1 in NSCLC models by inhibiting Treg cell conversion and proliferation. Journal for immunotherapy of cancer 2021 — PMC7931761.
PubMed PMID:2436037 — UniProt-cited evidence.
PubMed PMID:16177791 — UniProt-cited evidence.
PubMed PMID:15489334 — UniProt-cited evidence.