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.

Saccharomyces cerevisiae Trehalose-phosphatase (TPS2)

1-CSB-RP165694Ye(N)
  • EUR 733.20
  • EUR 370.80
  • EUR 2192.40
  • EUR 1126.80
  • EUR 1461.60
  • EUR 476.40
  • 100ug
  • 10ug
  • 1MG
  • 200ug
  • 500ug
  • 50ug
Description: Recombinant Saccharomyces cerevisiae Trehalose-phosphatase(TPS2),partial expressed in E.coli

Human Histone deacetylase 7 (HDAC7)

1-CSB-RP178994h(N)
  • EUR 456.00
  • EUR 256.80
  • EUR 1570.80
  • EUR 672.00
  • EUR 1047.60
  • EUR 314.40
  • 100ug
  • 10ug
  • 1MG
  • 200ug
  • 500ug
  • 50ug
Description: Recombinant Human Histone deacetylase 7(HDAC7),partial expressed in E.coli

Human Telomerase protein component 1 (TEP1)

1-CSB-RP180494h(N)
  • EUR 456.00
  • EUR 256.80
  • EUR 1570.80
  • EUR 672.00
  • EUR 1047.60
  • EUR 314.40
  • 100ug
  • 10ug
  • 1MG
  • 200ug
  • 500ug
  • 50ug
Description: Recombinant Human Telomerase protein component 1(TEP1),partial expressed in E.coli

Saccharomyces cerevisiae Neutral trehalase (NTH1)

1-CSB-RP181594Ye(N)
  • EUR 733.20
  • EUR 370.80
  • EUR 2192.40
  • EUR 1126.80
  • EUR 1461.60
  • EUR 476.40
  • 100ug
  • 10ug
  • 1MG
  • 200ug
  • 500ug
  • 50ug
Description: Recombinant Saccharomyces cerevisiae Neutral trehalase(NTH1),partial expressed in E.coli

Saccharomyces cerevisiae Acyl-CoA-binding protein (ACB1)

1-CSB-YP006519SVG(N)
  • EUR 814.80
  • EUR 402.00
  • EUR 2606.40
  • EUR 1261.20
  • EUR 1730.40
  • EUR 522.00
  • 100ug
  • 10ug
  • 1MG
  • 200ug
  • 500ug
  • 50ug
Description: Recombinant Saccharomyces cerevisiae Acyl-CoA-binding protein(ACB1) expressed in Yeast

Human Nuclear pore membrane glycoprotein 210 (NUP210)

1-CSB-EP016195HU(N)
  • EUR 456.00
  • EUR 256.80
  • EUR 1570.80
  • EUR 672.00
  • EUR 1047.60
  • EUR 314.40
  • 100ug
  • 10ug
  • 1MG
  • 200ug
  • 500ug
  • 50ug
Description: Recombinant Human Nuclear pore membrane glycoprotein 210(NUP210),partial expressed in E.coli

Clenbuterol Residues [BSA]

DAGA-004B 1mg
EUR 936

Clenbuterol Residues [HRP]

DAGA-004H 1mg
EUR 1404

Clenbuterol Residues [KLH]

DAGA-004K 1mg
EUR 1248

Chymotrypsin for Sequencing grade

C4001-010 4x25ug
EUR 375.6

Chymotrypsin for Sequencing grade

C4001-100 100ug
EUR 343.2

sequencing unit 33x45 cm

ESEQ1100-SYS ea
EUR 1842

sequencing system 20x50 cm

ESEQ1200-SYS ea
EUR 1842

Trypin for Mass & Sequencing

T9600-025 25ug
EUR 174

Trypin for Mass & Sequencing

T9600-100 100ug
EUR 262.8

Trypin for Mass & Sequencing

T9600-112 12x100ug
EUR 1988.4

Trypin for Mass & Sequencing

T9600-400 4x100ug
EUR 781.2

Clenbuterol residues ELISA Kit

DEIANJ44 96T
EUR 1039.2
Description: This ELISA kit is used for quantitative determination of Clenbuterol residues.

1730 10 SNAP-SEAL 10 OZ

1730-10 100/pk
EUR 96
Description: Disposable Plastic; Plastic Containers

99445-10 DCT 10 X 75MM

99445-10 250/pk
EUR 75.6
Description: Disposable Culture Tubes; DCT's, CGW

GSA 10

B5767-10 10 mg
EUR 274.8

SC-10

B6299-10 10 mg
EUR 255.6

MRT 10

B7685-10 10 mg
EUR 285.6

EpiNext Bisulfite Sequencing Kit (Illumina)

P-1056-12 12 Reactions
EUR 625.9

EpiNext Bisulfite Sequencing Kit (Illumina)

P-1056-24 24 Reactions
EUR 1225.4

SequaGel Sequencing System 1L Kit

NAT1136 1KIT
EUR 127.68

SequaGel Sequencing System 2.2L Kit

NAT1138 EACH
EUR 217.74

EpiNext Bisulfite Sequencing Kit (Illumina)

P-1056
  • EUR 1798.26
  • EUR 625.90
  • EUR 1225.40
  • 24 Reactions
  • 12 Reactions
  • 24 Reactions

Dynorphin A (1-10)-Gly-chloromethylketone

N-1605.0001 1.0mg
EUR 691.2
Description: Sum Formula: C60H95ClN20O12; CAS# [189002-98-0] net

Dynorphin A (1-10)-Gly-chloromethylketone

N-1605.0005 5.0mg
EUR 2648.4
Description: Sum Formula: C60H95ClN20O12; CAS# [189002-98-0] net

Sulfonamides residues ELISA Kit (OKAO00112)

OKAO00112 96 Wells
EUR 669.6
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

Fas C- Terminal Tripeptide

A1029-10 10 mg
EUR 477.6
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.

AI-10-49

A8694-10 10 mg
EUR 254.4
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 590.4
Description: Mouse monoclonal Keratin 10 antibody

MFZ 10-7

B5595-10 10 mg
EUR 420

TC ASK 10

B5728-10 10 mg
EUR 525.6

PSB 10 hydrochloride

B6923-10 10 mg
EUR 439.2

10-DEBC hydrochloride

B7105-10 10 mg
EUR 265.2
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.

KinaSorb™ 10

KE785-10 10 preps
EUR 553.2

Alkyne Phosphoramidite, 5'-terminal, 10 g

82260 10 g
EUR 918

PCR Clean Up for DNA Sequencing

BT5100 100preps
EUR 114.82

PCR Clean Up for DNA Sequencing

BT5101 1000Preps, 1000prep
EUR 553.3

N-Acetylglucosamine

NAG15-N 1 g
EUR 343.2

Histone H3 Peptide (residues 1-21) 

R-1003-200 200 ul
EUR 78.1

Histone H3 Peptide (residues 1-21) 

R-1003-400 400 ul
EUR 140.8

Histone H3 Peptide (residues 15-39) 

R-1005-100 100 ul
EUR 94.6

Histone H3 Peptide (residues 15-39) 

R-1005-200 200 ul
EUR 165

Histone H3 Peptide (residues 1-21) 

R-1003
  • EUR 267.06
  • EUR 78.10
  • EUR 140.80
  • 400 µl
  • 200 ul
  • 400 ul

Histone H3 Peptide (residues 15-39) 

R-1005
  • EUR 303.60
  • EUR 94.60
  • EUR 165.00
  • 200 µl
  • 100 ul
  • 200 ul

Amyloid Precursor C-Terminal Peptide

A1004-10 10 mg
EUR 442.8
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.

IL-10, murine recombinant

4156-10
EUR 294

IL-10, rat recombinant

4157-10
EUR 360

C-10, murine recombinant

4008-10
EUR 307.2

IL-10, human recombinant

4155-10
EUR 294

HG-10-102-01

B1262-10 10 mg
EUR 363.6
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 320.4

GFP Antibody, 10 uL

P601-10 - Ask for price

Individual Reaction Mix 10

G065-10 200 reactions
EUR 200.4

GSDMD Antibody - N-terminal

DF12275 200ul
EUR 420

TLR2 antibody (N-terminal)

70R-14928 50 ug
EUR 560.4
Description: Rabbit polyclonal TLR2 antibody (N-terminal)

TLE3 antibody (N-terminal)

20R-3004 100 ug
EUR 452.4
Description: Rabbit polyclonal TLE3 antibody (N-terminal)

p62 antibody (N-terminal)

20R-PP002 100 uL
EUR 690
Description: Guinea Pig polyclonal p62 antibody

N-terminal Arginylation Antibody

abx440096-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440097-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440098-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440099-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442905-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442906-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442907-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442908-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx443185-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443186-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443187-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443188-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443466-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443467-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443468-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443469-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx443747-100ug 100 ug
EUR 844.8

N-terminal Arginylation Antibody

abx443748-100ug 100 ug
EUR 844.8

N-terminal Arginylation Antibody

abx443749-100ug 100 ug
EUR 844.8

N-terminal Arginylation Antibody

abx443750-100ug 100 ug
EUR 844.8

N-terminal Arginylation Antibody

abx444028-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444029-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444030-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444031-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444309-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444310-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444311-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444312-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444590-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444591-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444592-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444593-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx444947-100ug 100 ug
EUR 760.8

N-terminal Arginylation Antibody

abx444948-100ug 100 ug
EUR 760.8

N-terminal Arginylation Antibody

abx444949-100ug 100 ug
EUR 760.8

N-terminal Arginylation Antibody

abx444950-100ug 100 ug
EUR 760.8

N-terminal Arginylation Antibody

abx440377-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440378-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440379-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440380-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440658-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440659-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440660-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440661-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440939-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440940-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440941-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx440942-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441220-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441221-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441222-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441223-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441501-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441502-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441503-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441504-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441782-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441783-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441784-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx441785-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442063-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442064-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442065-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442066-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442344-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx442345-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx442346-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx442347-100ug 100 ug
EUR 811.2

N-terminal Arginylation Antibody

abx442625-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442626-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442627-100ug 100 ug
EUR 828

N-terminal Arginylation Antibody

abx442628-100ug 100 ug
EUR 828

MyD88 Antibody / N-Terminal

R20327-0.1ML 100ul
EUR 409

SLC7A3 Antibody (N-Terminal)

R32985 100 ug
EUR 419

NSFL1C Antibody (N-Terminal)

F53995-0.05ML 0.05 ml
EUR 165

NSFL1C Antibody (N-Terminal)

F53995-0.2ML 0.2 ml
EUR 379

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

BR480-N 1PK, 10UNIT
EUR 98.1

TW-47-10 with 11 in. Canisters (10)

TW-47-10 1 Unit
EUR 1908
Description: TW-47-10 with 11 in. Canisters (10)

Carica papaya Papain (>10 U/ml)

CPP15-N-100 100 mg
EUR 270

7078D 10 PIPET 10ML STERILE

7078D-10 25/pk
EUR 310.8
Description: Disposable Pipets; Disposable Pipets, Serological, Misc

Beta-Lipotropin (1-10), porcine

A1014-10 10 mg
EUR 199.2
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 756
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 547.2
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 164.4

[bAla8]-Neurokinin A(4-10)

B6813-10 10 mg
EUR 1774.8

(10) Base holders and cases

BH-10 10 BOX
EUR 124
Description: (10) Base holders and cases

DNA Library Prep Kit for IIlumina Sequencing

K1475-12 12 Rxns
EUR 576

Histone H3 Peptide (residues 1-21), Biotinylated

R-1004-100 100 ul
EUR 78.1

Histone H3 Peptide (residues 1-21), Biotinylated

R-1004-200 200 ul
EUR 140.8

Histone H3 Peptide (residues 21-44), Biotinylated

R-1006-100 100 ul
EUR 119.9

Histone H3 Peptide (residues 21-44), Biotinylated

R-1006-200 200 ul
EUR 205.7

Histone H4 Peptide (residues 1-21), Biotinylated

R-1007-100 100 ul
EUR 119.9

Histone H4 Peptide (residues 1-21), Biotinylated

R-1007-200 200 ul
EUR 204.6

Histone H3 Peptide (residues 1-21), Biotinylated

R-1004
  • EUR 267.06
  • EUR 78.10
  • EUR 140.80
  • 200 µl
  • 100 ul
  • 200 ul

Histone H3 Peptide (residues 21-44), Biotinylated

R-1006
  • EUR 362.76
  • EUR 119.90
  • EUR 205.70
  • 200 µl
  • 100 ul
  • 200 ul

Histone H4 Peptide (residues 1-21), Biotinylated

R-1007
  • EUR 361.02
  • EUR 119.90
  • EUR 204.60
  • 200 µl
  • 100 ul
  • 200 ul

Histone H3 Peptide (residues 69-89), Biotinylated

R-1057 200 µl
EUR 267.06

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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