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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description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 701 to 750 of 3206 in total
description
Rank
measured
expected
final
Hugo
"LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 2021 0.0840355 0.364571 0.230505169 no value
"LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]" 2906 0.0662042 0.380173 0.174142298 MAN2B1
"MAGUK P55 SUBFAMILY MEMBER 2 (MPP2 PROTEIN) (DISCS, LARGE HOMOLOG 2). [SWISSPROT;Acc:Q14168]" 1276 0.123807 0.50235 0.246455658 MPP2
"MAGUK P55 SUBFAMILY MEMBER 3 (MPP3 PROTEIN) (DISCS, LARGE HOMOLOG 3). [SWISSPROT;Acc:Q13368]" 2023 0.112993 0.490447 0.230387789 MPP3
"MALATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.1.37). [SWISSPROT;Acc:P40926]" 2926 0.177425 1.08227 0.163937834 MDH2
"MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 4.1.1.9) (MCD). [SWISSPROT;Acc:O95822]" 831 0.0344093 0.131824 0.261024548 MLYCD
"MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE IB (EC 3.2.1.113) (PROCESSING ALPHA-1,2-MANNOSIDASE IB) (ALPHA-1,2-MANNOSIDASE IB) (MANNOSIDASE ALPHA CLASS 1A MEMBER 2). [SWISSPROT;Acc:O60476]" 3109 0.116081 1.26306 0.091904581 no value
"MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]" 3152 0.0654743 1.00142 0.065381458 MAGEB6B
"MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]" 3135 0.066175 1.01213 0.065381917 MAGED4
"METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.9) (MTFMT). [SWISSPROT;Acc:Q96DP5]" 2551 0.510943 2.38162 0.214535904 MTFMT
"METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL PRECURSOR (EC 1.2.1.27) (MMSDH). [SWISSPROT;Acc:Q02252]" 940 0.0637409 0.248593 0.256406657 ALDH6A1
"MICROTUBULE-ACTIN CROSSLINKING FACTOR 1, ISOFORM 4. [SWISSPROT;Acc:Q96PK2]" 1574 0.0946162 0.392702 0.240936384 MACF1
"MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" 1429 0.0850122 0.348604 0.243864672 MAPRE2
"MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" 2499 0.235517 1.09378 0.215323923 PMPCA
"MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 2500 0.208649 0.969013 0.215321157 PMPCB
"MMS19-LIKE (MET18 HOMOLOG, S. CEREVISIAE); HOMOLOG OF YEAST MMS19; MMS19 (MET18 S. CEREVISIAE)-LIKE. [RefSeq;Acc:NM_022362]" 2146 0.155283 0.682226 0.227612258 MMS19
"MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" 3166 0.081705 1.26263 0.064710168 no value
"MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" 3163 0.0816437 1.26168 0.064710307
"MYOSIN HEAVY CHAIN, FAST SKELETAL MUSCLE, EMBRYONIC (MUSCLE EMBRYONIC MYOSIN HEAVY CHAIN) (SMHCE). [SWISSPROT;Acc:P11055]" 3162 0.0727992 1.125 0.0647104 MYH3
"MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 1 (MYOSIN HEAVY CHAIN IIX/D) (MYHC-IIX/D). [SWISSPROT;Acc:P12882]" 3158 0.0741473 1.14583 0.064710559 MYH1
"MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 2 (MYOSIN HEAVY CHAIN IIA) (MYHC-IIA). [SWISSPROT;Acc:Q9UKX2]" 3164 0.0739839 1.14331 0.064710271 MYH2
"MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, EXTRAOCULAR (MYHC-EO). [SWISSPROT;Acc:Q9UKX3]" 3161 0.0720434 1.11332 0.064710416 MYH13
"MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, FETAL (MYOSIN HEAVY CHAIN IIB) (MYHC-IIB). [SWISSPROT;Acc:Q9Y623]" 3165 0.0736571 1.13826 0.06471026 MYH4
"MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, PERINATAL (MYHC-PERINATAL). [SWISSPROT;Acc:P13535]" 3159 0.0736775 1.13857 0.064710558 MYH8
"MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 820 0.0259096 0.0991465 0.261326421 no value
"MYOSIN LIGHT CHAIN 1, SKELETAL MUSCLE ISOFORM (MLC1F) (A1 CATALYTIC) (ALKALI). [SWISSPROT;Acc:P05976]" 821 0.0255016 0.0975853 0.261326245 MYL1
"MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM (MLC1SA) (ALKALI). [SWISSPROT;Acc:P14649]" 818 0.0296703 0.113537 0.261327144 MYL6
"MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE B/VENTRICULAR ISOFORM (MLC1SB) (ALKALI). [SWISSPROT;Acc:P08590]" 819 0.025294 0.0967906 0.26132703 MYL3
"MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]" 3131 0.163856 2.39209 0.068499095 no value
"N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [SWISSP" 999 0.036112 0.141665 0.254911234 B3GNT1
"NADH-UBIQUINONE OXIDOREDUCTASE 13 KDA-A SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-13KD-A) (CI-13KD-A). [SWISSPROT;Acc:O75380]" 817 0.0296703 0.113537 0.261327144 NDUFS6
"NADH-UBIQUINONE OXIDOREDUCTASE 18 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-18 KDA) (CI-18 KDA) (COMPLEX I- AQDQ) (CI-AQDQ). [SWISSPROT;Acc:O43181]" 5 0.489705 0.74385 0.658338375 NDUFS4
"NADH-UBIQUINONE OXIDOREDUCTASE 23 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-23KD) (CI-23KD) (TYKY SUBUNIT). [SWISSPROT;Acc:O00217]" 332 0.0963108 0.337743 0.285160018 NDUFS8
"NADPH:ADRENODOXIN OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.18.1.2) (ADRENODOXIN REDUCTASE) (AR) (FERREDOXIN-NADP(+) REDUCTASE). [SWISSPROT;Acc:P22570]" 2092 0.0601271 0.262913 0.228695804 FDXR
"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]" 2630 0.0142351 0.0677865 0.209999041 CHRNA2
"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]" 2635 0.0132921 0.0632961 0.20999872 CHRNA3
"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]" 2632 0.0186658 0.0888852 0.209998965 CHRNA4
"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]" 2631 0.0131531 0.0626341 0.209999026 CHRNA6
"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-7 CHAIN PRECURSOR. [SWISSPROT;Acc:P36544]" 842 0.077721 0.298119 0.260704618 CHRNA7
"NEUTRAL AND BASIC AMINO ACID TRANSPORT PROTEIN RBAT (B(0,+)-TYPE AMINO ACID TRANSPORT PROTEIN) (NBAT) (D2H). [SWISSPROT;Acc:Q07837]" 1812 0.0214423 0.0914656 0.234430212 SLC3A1
"NONSPECIFIC LIPID-TRANSFER PROTEIN, MITOCHONDRIAL PRECURSOR (NSL-TP) (STEROL CARRIER PROTEIN 2) (SCP-2) (STEROL CARRIER PROTEIN X) (SCP-X) (SCPX). [SWISSPROT;Acc:P22307]" 108 0.192957 0.526194 0.366703155 SCP2
"NUCLEAR FACTOR ERYTHROID 2 RELATED FACTOR 1 (NF-E2 RELATED FACTOR 1) (NFE2-RELATED FACTOR 1) (NUCLEAR FACTOR, ERYTHROID DERIVED 2, LIKE 1) (TRANSCRIPTION FACTOR 11) (TRANSCRIPTION FACTOR HBZ17) (TRANSCRIPTION FACTOR LCR-F1) (LOCUS CONTROL REGION-FACTOR 1)" 2671 0.0693641 0.331516 0.209233039 NFE2L1
"NUCLEAR FACTOR, INTERLEUKIN 3 REGULATED. [RefSeq;Acc:NM_005384]" 781 0.150787 0.573002 0.263152659 NFIL3
"NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE-1 (NIPP-1) (PROTEIN PHOSPHATASE 1, REGULATORY INHIBITOR SUBUNIT 8) [INCLUDES: ACTIVATOR OF RNA DECAY (EC 3.1.4.-) (ARD-1)]. [SWISSPROT;Acc:Q12972]" 1665 0.179673 0.752395 0.238801427 PPP1R8
"NUCLEOLAR PROTEIN FAMILY A, MEMBER 1; GAR1 PROTEIN. [RefSeq;Acc:NM_018983]" 256 0.11305 0.363171 0.311285868 NOLA1
"NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [RefSeq;Acc:NM_017838]" 1714 0.0909039 0.382985 0.237356293 NOLA2
"NUCLEOSTEMIN; PUTATIVE NUCLEOTIDE BINDING PROTEIN, ESTRADIOL-INDUCED. [RefSeq;Acc:NM_014366]" 1283 0.856366 3.47989 0.246089963 GNL3
"OLIGOPEPTIDE TRANSPORTER, KIDNEY ISOFORM (PEPTIDE TRANSPORTER 2) (KIDNEY H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 2). [SWISSPROT;Acc:Q16348]" 278 0.33474 1.10122 0.303971958 SLC15A2
"OLIGOPEPTIDE TRANSPORTER, SMALL INTESTINE ISOFORM (PEPTIDE TRANSPORTER 1) (INTESTINAL H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 1). [SWISSPROT;Acc:P46059]" 280 0.245451 0.807655 0.303905752 SLC15A1
"OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [SWISSPROT;Acc:Q9Y3B8]" 949 0.0337699 0.131705 0.256405603 REXO2

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/