Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Background: Much learning has emerged as a versatile approach for predicting complex biological phenomena. However, the utility of biological discoveries so far been limited, given that generic neural network in providing some insight into the biological mechanisms that underlie successful predictions.

Here we demonstrate in-depth study on the biological network, where each node has an equivalent molecules, such as proteins or genes, and each edge has a mechanistic interpretation, such as regulatory interactions along the signal path.


Results: With the knowledge-primed neural network (KPNNs), we exploit the ability of deep learning algorithm to assign significant weight in the multi-layered network, thus broadly applicable approach to learning in the interpretation. We present a method of learning that increases the interpretability of KPNNs trained by stabilizing the node weights in the presence of redundancy, improve the interpretability quantitative node weights, and control for connectivity are uneven in biological tissue. We validate KPNNs simulated data with known ground truth and show their practical use and utility in five applications with single-cell biology of RNA-seq data for cancer and immune cells.


Conclusions: We introduce KPNNs as a method that combines the predictive power of deep learning with biological tissue interpretability. While shown here at the single-cell sequencing data, this method is broadly relevant to other research fields in which domain knowledge before it can be represented as a network.


neuroendocrine neoplasms (NENs) is a clinical cancer incomplete diverse and characterized challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancer. More recently, morphology-based classification framework to evaluate NENs from different anatomical sites proposed by the experts, the need for enhanced integration of molecular data.

Here, we collected 378 miRNA expression profiling to examine the classification of Nen through a comprehensive miRNA profiling and data mining. The following data preprocessing, our final study cohort included 221 and 114 Nen-Nen non samples, representing 15 Nen type of pathological and 5 non-site-matched control group Nen.

 Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Use Whole Genome Sequencing data for First Silico Evaluation Test Specificity of RT-qPCR Used for SARS-CoV-2 Detection

Disease coronavirus Flow 2019 (COVID-19) pandemic started in December 2019. COVID 19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, a limited number of SARS-CoV-2 genome is available as RT-qPCR method was first developed in January 2020 to early in silico evaluation of specificity and to verify whether the target locus highly conserved.

Now that the genome data more completely available, we use the tools of bioinformatics filtered and total 4755 publicly available SARS-CoV-2 genome, download at two different time points to evaluate the specificity 12 tests RT-qPCR (comprised of a total of 30 primary and probe sets) used for SARS-CoV-2 detection and the impact of the genetic evolution of the virus’ on four of them.

Chymotrypsin for Sequencing grade

C4001-010 4x25ug
EUR 313.00

Chymotrypsin for Sequencing grade

C4001-100 100ug
EUR 286.00

sequencing unit 33x45 cm

ESEQ1100-SYS ea
EUR 1535.00

sequencing system 20x50 cm

ESEQ1200-SYS ea
EUR 1535.00

Trypin for Mass & Sequencing

T9600-025 25ug
EUR 145.00

Trypin for Mass & Sequencing

T9600-100 100ug
EUR 219.00

Trypin for Mass & Sequencing

T9600-112 12x100ug
EUR 1657.00

Trypin for Mass & Sequencing

T9600-400 4x100ug
EUR 651.00

Clenbuterol residues ELISA Kit

DEIANJ44 96T
EUR 866.00
Description: This ELISA kit is used for quantitative determination of Clenbuterol residues.

SequaGel Sequencing System 1L Kit

NAT1136 1KIT
EUR 143.00

SequaGel Sequencing System 2.2L Kit

NAT1138 EACH
EUR 211.00

Sulfonamides residues ELISA Kit (OKAO00112)

OKAO00112 96 Wells
EUR 558.00
Description: Description of target: The related sulfinamides (R(S=O)NHR) are amides of sulfinic acids (R(S=O)OH) (see sulfinyl). Chiral sulfinamides such as tert-butanesulfinamide, p-toluenesulfinamide and 2,4,6-trimethylbenzenesulfinamide are relevant to asymmetric synthesis.;Species reactivity: General;Application: ;Assay info: Assay Methodology: Competitive Inhibition ELISA;Sensitivity:
ComponentAmount
Tissue0.4 ppb
Honey, egg0.4 ppb
Serum, urine1.6 ppb
Milk8 ppb

99445-10 DCT 10 X 75MM

99445-10 250/pk
EUR 63.00
Description: Disposable Culture Tubes; DCT's, CGW

1730 10 SNAP-SEAL 10 OZ

1730-10 100/pk
EUR 80.00
Description: Disposable Plastic; Plastic Containers

GSA 10

B5767-10 10 mg
EUR 229.00

SC-10

B6299-10 10 mg
EUR 213.00

MRT 10

B7685-10 10 mg
EUR 238.00

Dynorphin A (1-10)-Gly-chloromethylketone

N-1605.0001 1.0mg
EUR 576.00
Description: Sum Formula: C60H95ClN20O12; CAS# [189002-98-0] net

Dynorphin A (1-10)-Gly-chloromethylketone

N-1605.0005 5.0mg
EUR 2207.00
Description: Sum Formula: C60H95ClN20O12; CAS# [189002-98-0] net

PCR Clean Up for DNA Sequencing

BT5100 100preps
EUR 95.68
  • Product category: PCR Related/PCR Kits (Cleanup)

PCR Clean Up for DNA Sequencing

BT5101 1000Preps, 1000prep
EUR 461.08
  • Product category: PCR Related/PCR Kits (Cleanup)

Histone H3 Peptide (residues 1-21)

R-1003 400 µl
EUR 222.55
Description: Ask the seller for details

Histone H3 Peptide (residues 15-39)

R-1005 200 µl
EUR 253.00
Description: kits suitable for this type of research

TC ASK 10

B5728-10 10 mg
EUR 438.00

PSB 10 hydrochloride

B6923-10 10 mg
EUR 366.00

MFZ 10-7

B5595-10 10 mg
EUR 350.00

10-DEBC hydrochloride

B7105-10 10 mg
EUR 221.00
Description: 10-DEBC hydrochloride is a selective inhibitor of Akt (or termed PKB) [1], with an IC50 value of approximate 48 ?M [2].Akt is a type of serine/threonine kinase. It phosphorylates and inactivates components in the apoptotic machinery, including Caspase 9 and BAD.

AI-10-49

A8694-10 10 mg
EUR 212.00
Description: AI-10-49 is a selective inhibitor of CBF? -SMMHC and RUNX1 interaction with a FRET IC50 value of 260nM. AI-10-49 restores RUNX1 transcriptional activity, displays favorable pharmacokinetics, and delays leukemia progression in mice.

Keratin 10 antibody

10-2541 250 ug
EUR 492.00
Description: Mouse monoclonal Keratin 10 antibody

KinaSorb™ 10

KE785-10 10 preps
EUR 461.00

Fas C- Terminal Tripeptide

A1029-10 10 mg
EUR 398.00
Description: Fas C- Terminal Tripeptide,(C16H29N3O6), a tri-peptide with the sequence AC-SER-LEU-VAL-OH, it?s the C-terminal tripeptide of Fas, MW= 359.4.

Alkyne Phosphoramidite, 5'-terminal, 10 g

82260 10 g
EUR 765.00

DNA Library Prep Kit for IIlumina Sequencing

K1475-12 12 Rxns
EUR 480.00

Histone H3 Peptide (residues 69-89), Biotinylated

R-1057 200 µl
EUR 222.55
Description: kits suitable for this type of research

Histone H3 Peptide (residues 1-21), Biotinylated

R-1004 200 µl
EUR 222.55
Description: The best epigenetics products

Histone H3 Peptide (residues 21-44), Biotinylated

R-1006 200 µl
EUR 302.30
Description: fast delivery possible

Histone H4 Peptide (residues 1-21), Biotinylated

R-1007 200 µl
EUR 300.85
Description: reagents widely cited

HG-10-102-01

B1262-10 10 mg
EUR 303.00
Description: HG-10-102-01 is a potent and selective inhibitor of leucine-rich repeat kinase 2 (LRRK2) with the IC50 values of 20.3nM and 3.2nM for wild type LRRK2 and LRRK2 [G1019S], respectively [1].

Ro 10-5824 dihydrochloride

B7019-10 10 mg
EUR 267.00

Individual Reaction Mix 10

G065-10 200 reactions
EUR 167.00

IL-10, human recombinant

4155-10
EUR 245.00

IL-10, murine recombinant

4156-10
EUR 245.00

IL-10, rat recombinant

4157-10
EUR 300.00

C-10, murine recombinant

4008-10
EUR 256.00

GFP Antibody, 10 uL

P601-10 NULL
EUR NULL

N-Acetylglucosamine

NAG15-N 1 g
EUR 286.00

Amyloid Precursor C-Terminal Peptide

A1004-10 10 mg
EUR 369.00
Description: Amyloid precursor c-terminal peptide (APP) (C86H118N20O27S) has the amino acid sequence Gly-Tyr-Glu-Asn-Pro-Thr-Tyr-Lys-Phe-Phe-Glu-Gln-Met-Gln-Asn. Although it has been implicated as a regulator of synapse formation, neural plasticity and iron export, the primary function of APP is not known.

48-Well 4ml U-Shaped Deep-Well Plates, 10/Bag

BR480-N 1PK, 10UNIT
EUR 81.75
  • Product category: Labware/Multiwell Plates/48-Well

Carica papaya Papain (>10 U/ml)

CPP15-N-100 100 mg
EUR 225.00

N-terminal Arginylation Antibody

abx440096-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440097-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440098-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440099-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440377-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440378-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440379-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440380-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440658-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440659-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440660-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440661-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440939-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440940-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440941-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx440942-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441220-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441221-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441222-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441223-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441501-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441502-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

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EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441504-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441782-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441783-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441784-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx441785-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442063-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442064-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442065-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442066-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442344-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442345-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442346-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442347-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442625-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442626-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442627-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442628-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442905-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442906-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442907-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx442908-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443185-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443186-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443187-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443188-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443466-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443467-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443468-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443469-100ug 100 ug
EUR 676.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443747-100ug 100 ug
EUR 704.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443748-100ug 100 ug
EUR 704.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443749-100ug 100 ug
EUR 704.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx443750-100ug 100 ug
EUR 704.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444028-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444029-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444030-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444031-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444309-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444310-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444311-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444312-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444590-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444591-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444592-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444593-100ug 100 ug
EUR 690.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444947-100ug 100 ug
EUR 634.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444948-100ug 100 ug
EUR 634.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444949-100ug 100 ug
EUR 634.00
  • Shipped within 5-12 working days.

N-terminal Arginylation Antibody

abx444950-100ug 100 ug
EUR 634.00
  • Shipped within 5-12 working days.

TLE3 antibody (N-terminal)

20R-3004 100 ug
EUR 377.00
Description: Rabbit polyclonal TLE3 antibody (N-terminal)

p62 antibody (N-terminal)

20R-PP002 100 uL
EUR 575.00
Description: Guinea Pig polyclonal p62 antibody

TLR2 antibody (N-terminal)

70R-14928 50 ug
EUR 467.00
Description: Rabbit polyclonal TLR2 antibody (N-terminal)

[bAla8]-Neurokinin A(4-10)

B6813-10 10 mg
EUR 1479.00

Beta-Lipotropin (1-10), porcine

A1014-10 10 mg
EUR 166.00
Description: Morphine-like substances exist in brain or the pituitary of various species. Beta-lipotropin (beta-LPH) was found to contain within its C-terminal sequence the primary structure of these peptides.

Amyloid ?-Peptide (10-20) (human)

A1038-10 10 mg
EUR 630.00
Description: The amyloid ?-peptide (A?) has a central role in initiating neurodegeneration in Alzheimer disease (AD) 1. It is widely believed to be an incidental catabolic byproduct of the amyloid ? protein precursor (APP) with no normal physiological function.

Amyloid ?-peptide (10-35), amide

A1102-10 10 mg
EUR 456.00
Description: Amyloid ?-protein (10-35) was used as a trunCated peptide model for the full-length amyloid ?-proteins (1-40) and (1-42) in high-resolution structural studies. In contrast to the full-length amyloid ?-proteins, amyloid ?-protein (10-35) allowed the contro

BSA (10% in H?O)

2119-10
EUR 137.00

7078D 10 PIPET 10ML STERILE

7078D-10 25/pk
EUR 259.00
Description: Disposable Pipets; Disposable Pipets, Serological, Misc

TruStrip RDT Sulfonamides residues (SAs) rapid test strips, results is 2-10 mins, 50 strips/pk

DE-100090-RDT 1 pk
EUR 651.00

MIP-1?/CCL9/10, murine recombinant

7174-10
EUR 207.00

Atholate™, protein hydrolysate, 10 kg

0134-10 10 kg
EUR 1982.00

Ethyl-β-D-glucuronide, 10 mg

0901-10 10 mg
EUR 554.00

Ethyl sulfate, sodium salt, 10 mg

0902-10 10 mg
EUR 132.00

Propyl-β-D-glucuronide, 10 mg

0903-10 10 mg
EUR 554.00

Human CellExp? IL-10, Human Recombinant

6466-10
EUR 343.00

Human IP-10 ELISPOT antibody pair

CT470-10 10-plate
EUR 528.00

Monkey IP-10 ELISA antibody pair

CT555-10 10-plate
EUR 547.00

Human IP-10 ELISA antibody pair

CT572-10 10-plate
EUR 547.00

Monkey IL-10 ELISPOT antibody pair

CT615-10 10-plate
EUR 528.00

Human IL-10 ELISPOT antibody pair

CT645-10 10-plate
EUR 528.00

Mouse IL-10 ELISPOT antibody pair

CT658-10 10-plate
EUR 528.00

Monkey IL-10 ELISA antibody pair

CT715-10 10-plate
EUR 547.00

Human IL-10 ELISA antibody pair

CT745-10 10-plate
EUR 547.00

Mouse IL-10 ELISA antibody pair

CT765-10 10-plate
EUR 547.00

10x17 cellogel 250µ (10)

EHCA1200-SH01-10 ea
EUR 56.00

10x17 cellogel 200µ (10)

EHCA1200-SH02-10 ea
EUR 56.00

10x17 cellogel 190µ (10)

EHCA1200-SH03-10 ea
EUR 56.00

10x17 cellogel 500µ (10)

EHCA1200-SH04-10 ea
EUR 69.00

16.5x14 cellogel 250µ (10)

EHCA1200-SH07-10 ea
EUR 69.00

16.5x14 cellogel 200µ (10)

EHCA1200-SH08-10 ea
EUR 69.00

16.5x14 cellogel 500µ (10)

EHCA1200-SH10-10 ea
EUR 78.00

17x17 cellogel 250µ (10)

EHCA1200-SH12-10 ea
EUR 87.00

17x17 cellogel 200µ (10)

EHCA1200-SH13-10 ea
EUR 87.00

17x17 cellogel 500µ (10)

EHCA1200-SH15-10 ea
EUR 105.00

20.5x20.5 cellogel 250µ (10)

EHCA1200-SH17-10 ea
EUR 214.00

20.5x20.5 cellogel 200µ (10)

EHCA1200-SH18-10 ea
EUR 214.00

20.5x20.5 cellogel 500µ (10)

EHCA1200-SH20-10 ea
EUR 260.00

Exclusivity This method was also assessed using the human reference genome and the genomes of closely related 2624 other respiratory viruses. Specificity of this test is generally good and stable over time. The exception is the method was first developed by the Chinese Center for Disease Control and Prevention (CDC), which showed three primary discrepancy is present in 358 SARS-CoV-2 genome sequencing, especially in Europe from February 2020 onwards.

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