Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2358 to 2407 of 3206 in total
Rank
description
measured
expected
final
Hugo
2358 PROTOCADHERIN 15 PRECURSOR. [SWISSPROT;Acc:Q96QU1] 0.0344025 0.156164 0.220297252 PCDH15
2359 GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C). [SWISSPROT;Acc:P20142] 0.0442218 0.200737 0.220297205 PGC
2360 ZINC FINGER PROTEIN GLI3. [SWISSPROT;Acc:P10071] 0.0204267 0.0927234 0.220297142 GLI3
2361 SUPPRESSOR OF FUSED. [RefSeq;Acc:NM_016169] 0.152908 0.694099 0.220297105 SUFU
2362 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 1; GLVR-1; PIT-1; GIBBON APE LEUKEMIA VIRUS RECEPTOR 1. [RefSeq;Acc:NM_005415]" 0.0465225 0.211181 0.220296807 SLC20A1
2363 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 2; GLVR-2; PIT-2; GIBBON APE LEUKEMIA VIRUS RECEPTOR 2; MURINE LEUKEMIA VIRUS, AMPHOTROPIC; RECEPTOR. [RefSeq;Acc:NM_006749]" 0.0378408 0.171772 0.220296672 SLC20A2
2364 LIMB REGION 1 PROTEIN; LIMB REGION 1. [RefSeq;Acc:NM_022458] 0.0589602 0.26764 0.220296667 LMBR1
2365 FARNESYL PYROPHOSPHATE SYNTHETASE (FPP SYNTHETASE) (FPS) (FARNESYL DIPHOSPHATE SYNTHETASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10)]. [SWISSPROT;Acc:P14324] 0.334917 1.5203 0.220296652 FDPS
2366 PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790] 0.0604093 0.274218 0.220296625 no value
2367 LIPOCALIN-INTERACTING MEMBRANE RECEPTOR. [RefSeq;Acc:NM_018113] 0.0719255 0.326494 0.220296545 LMBR1L
2368 TRANSCRIPTION INITIATION FACTOR TFIID 100 KDA SUBUNIT (TAFII-100) (TAFII100). [SWISSPROT;Acc:Q15542] 0.331362 1.50518 0.220147756 TAF5
2369 TRANS-PRENYLTRANSFERASE; POLYPRENYL PYROPHOSPHATE SYNTHETASE. [RefSeq;Acc:NM_014317] 0.294256 1.3369 0.220103224 PDSS1
2370 "TRYPTOPHANYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.2) (TRYPTOPHAN--TRNA LIGASE) (TRPRS) ((MT)TRPRS). [SWISSPROT;Acc:Q9UGM6]" 0.0775947 0.352624 0.220049401 WARS2
2371 TRYPTOPHANYL-TRNA SYNTHETASE (EC 6.1.1.2) (TRYPTOPHAN--TRNA LIGASE) (TRPRS) (IFP53) (HWRS). [SWISSPROT;Acc:P23381] WARS
2372 RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] 0.327497 1.48829 0.220049184 no value
2373 LENG5 PROTEIN. [RefSeq;Acc:NM_024075] 0.0517945 0.235377 0.220049113 TSEN34
2374 0.0516003 0.234495 0.220048615 TSEN2
2375 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 0.0258973 0.117689 0.220048603 no value
2376 THIOREDOXIN-LIKE; PKC-INTERACTING COUSIN OF THIOREDOXIN. [RefSeq;Acc:NM_006541] 0.0698995 0.317655 0.22004848 GLRX3
2377 0.271141 1.23303 0.219898137 RIC8A
2378 0.223975 1.01863 0.219878661 RIC8B
2379 BIOTIN--PROTEIN LIGASE (EC 6.3.4.-) (BIOTIN APO-PROTEIN LIGASE) [INCLUDES: BIOTIN--[METHYLMALONYL-COA-CARBOXYLTRANSFERASE] LIGASE (EC 6.3.4.9); BIOTIN--[PROPIONYL-COA-CARBOXYLASE [ATP-HYDROLYZING]] LIGASE (EC 6.3.4.10) (HOLOCARBOXYLASE SYNTHETASE) (HCS); 0.18221 0.828912 0.219818268 HLCS
2380 MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 3 (MOLYBDOPTERIN SYNTHASE SULFURYLASE) (MPT SYNTHASE SULFURYLASE). [SWISSPROT;Acc:O95396] 0.275917 1.25591 0.219694883 MOCS3
2381 0.206722 0.940952 0.219694522 USP52
2382 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FES/FPS (EC 2.7.1.112) (C-FES). [SWISSPROT;Acc:P07332] 0.0453043 0.206215 0.219694494 FES
2383 60S RIBOSOMAL PROTEIN L29 (CELL SURFACE HEPARIN BINDING PROTEIN HIP). [SWISSPROT;Acc:P47914] 0.0507615 0.231055 0.219694445 RPL29
2384 ANAPHASE-PROMOTING COMPLEX SUBUNIT 10; ANAPHASE-PROMOTING COMPLEX 10. [RefSeq;Acc:NM_014885] 0.078258 0.356213 0.219694396 ANAPC10
2385 0.0280218 0.127549 0.219694392 C14orf153
2386 MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2 LARGE SUBUNIT (MOLYBDOPTERIN SYNTHASE LARGE SUBUNIT) (MPT SYNTHASE LARGE SUBUNIT) (MOCS2B) (MOCO1- B). [SWISSPROT;Acc:O96007] MOCS2
2387 URM1
2388 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FER (EC 2.7.1.112) (P94-FER) (C-FER). [SWISSPROT;Acc:P16591] 0.0558685 0.254301 0.219694378 FER
2389 "SUCCINYL-COA LIGASE [GDP-FORMING] ALPHA-CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.2.1.4) (SUCCINYL-COA SYNTHETASE, ALPHA CHAIN) (SCS-ALPHA). [SWISSPROT;Acc:P53597]" 0.245024 1.11536 0.219681538 SUCLG1
2390 "SUCCINYL-COA LIGASE [ADP-FORMING] BETA-CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.2.1.5) (SUCCINYL-COA SYNTHETASE, BETAA CHAIN) (SCS-BETAA) (ATP- SPECIFIC SUCCINYL-COA SYNTHETASE BETA SUBUNIT). [SWISSPROT;Acc:Q9P2R7]" SUCLA2
2391 "ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P30049]" 0.301597 1.37291 0.219677182 ATP5D
2392 GUANYLATE KINASE (EC 2.7.4.8) (GMP KINASE). [SWISSPROT;Acc:Q16774] 0.353823 1.61155 0.219554466 GUK1
2393 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1G). [SWISSPROT;Acc:P36873] 0.518333 2.36093 0.219546111 PPP1CC
2394 "BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 0.106596 0.485769 0.219437634 no value
2395 0.0914148 0.416755 0.219349018 MARS2
2396 SQUALENE MONOOXYGENASE (EC 1.14.99.7) (SQUALENE EPOXIDASE) (SE). [SWISSPROT;Acc:Q14534] 0.131761 0.60095 0.219254514 SQLE
2397 KYNURENINE 3-MONOOXYGENASE (KYNURENINE 3-HYDROXYLASE). [RefSeq;Acc:NM_003679] 0.132423 0.60397 0.219254268 KMO
2398 UBIQUINONE BIOSYNTHESIS MONOOXGENASE COQ6 (EC 1.14.13.-) (CGI-10). [SWISSPROT;Acc:Q9Y2Z9] COQ6
2399 WILLIAMS BEUREN SYNDROME CRITICAL REGION 20A ISOFORM 2; NOL1/NOP2/SUN GENE FAMILY MEMBER; WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY A; WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20. [RefSeq;Acc:NM_018044] 0.100955 0.460869 0.219053571 NSUN5
2400 NSUN2
2401 WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 0.0801834 0.366045 0.219053395 no value
2402 WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [RefSeq;Acc:NM_032158] 0.0859883 0.392545 0.219053357 NSUN5B
2403 PROHIBITIN. [SWISSPROT;Acc:P35232] 0.26817 1.22481 0.218948245 PHB
2404 REPRESSOR OF ESTROGEN RECEPTOR ACTIVITY; B-CELL ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007273] no value
2405 INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] 0.0252512 0.115441 0.218736844 ITM2A
2406 INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] 0.0256055 0.117061 0.218736385 ITM2C
2407 INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287] 0.0308129 0.140868 0.21873598 ITM2B

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/