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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expected Gene Rank measured description final Hugo
Results: HTML CSV LaTeX Showing element 2002 to 2051 of 3206 in total
expected
Rank
measured
description
final
Hugo
0.783008 1816 0.183433 UNC-119 PROTEIN HOMOLOG (RETINAL PROTEIN 4) (HRG4). [SWISSPROT;Acc:Q13432] 0.234267083 UNC119
0.78389 782 0.206261 SYNTAXIN 12. [RefSeq;Acc:NM_177424] 0.263124928 STX12
0.784198 1382 0.191835 0.24462572 DDX55
0.784403 2264 0.174876 RIBONUCLEASE P PROTEIN SUBUNIT P30 (EC 3.1.26.5) (RNASEP PROTEIN P30) (RNASE P SUBUNIT 2). [SWISSPROT;Acc:P78346] 0.222941524 RPP30
0.784548 306 0.232016 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652] 0.295732065 no value
0.785148 3126 0.0577935 "BETA-1,4 MANNOSYLTRANSFERASE. [RefSeq;Acc:NM_019109]" 0.073608415 ALG1
0.785612 368 0.219762 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H (HNRNP H). [SWISSPROT;Acc:P31943] 0.279733507 HNRPH1
0.7865 3206 0.000173011 0.000219976 no value
0.787708 1786 0.18522 "ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY-TYPE ARGINASE). [SWISSPROT;Acc:P78540]" 0.235137894 ARG2
0.788327 2437 0.171257 ANAPHASE-PROMOTING COMPLEX SUBUNIT 2; ANAPHASE-PROMOTING COMPLEX 2. [RefSeq;Acc:NM_013366] 0.217241069 ANAPC2
0.789676 3106 0.0728267 NEUROGENIC DIFFERENTIATION FACTOR 4 (NEUROD4). [SWISSPROT;Acc:Q9HD90] 0.09222352 NEUROD4
0.789739 2097 0.180388 URIDINE KINASE-LIKE 1. [SWISSPROT;Acc:Q9NWZ5] 0.228414704 no value
0.790803 1888 0.184055 PRP18 PRE-MRNA PROCESSING FACTOR 18 HOMOLOG. [RefSeq;Acc:NM_003675] 0.232744438 PRPF18
0.792735 2249 0.176971 60S RIBOSOMAL PROTEIN L15. [SWISSPROT;Acc:P39030] 0.223241058 RPL15
0.793116 1445 0.193092 GLUTAMINYL-TRNA SYNTHETASE (EC 6.1.1.18) (GLUTAMINE--TRNA LIGASE) (GLNRS). [SWISSPROT;Acc:P47897] 0.243459973 QARS
0.793992 1137 0.198834 PHOSPHOLIPID SCRAMBLASE 4 (PL SCRAMBLASE 4) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4). [SWISSPROT;Acc:Q9NRQ2] 0.250423178 PLSCR4
0.794014 369 0.222111 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H' (HNRNP H') (FTP-3). [SWISSPROT;Acc:P55795] 0.279731844 HNRPH2
0.794482 469 0.218407 "TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [SWISSPROT;Acc:Q9NVH6]" 0.274904907 TMLHE
0.795244 2493 0.171407 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] 0.215540136 SH3GL3
0.79556 1136 0.199227 PHOSPHOLIPID SCRAMBLASE 3 (PL SCRAMBLASE 3) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 3). [SWISSPROT;Acc:Q9NRY6] 0.250423601 no value
0.796037 1626 0.190544 "CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" 0.239365758 PRKACG
0.797115 786 0.209282 SYNTAXIN 7. [SWISSPROT;Acc:O15400] 0.262549318 STX7
0.797256 531 0.216511 RNA-BINDING REGION CONTAINING PROTEIN 1 (HSRNASEB) (SSDNA BINDING PROTEIN SEB4) (CLL-ASSOCIATED ANTIGEN KW-5). [SWISSPROT;Acc:Q9H0Z9] 0.271570236 RBM38
0.799038 226 0.253265 VINCULIN (METAVINCULIN). [SWISSPROT;Acc:P18206] 0.316962397 VCL
0.799962 255 0.249321 EXOCYST COMPLEX COMPONENT SEC10 (HSEC10). [SWISSPROT;Acc:O00471] 0.311666054 EXOC5
0.800978 2501 0.172401 SH3-CONTAINING GRB2-LIKE PROTEIN 1 (SH3 DOMAIN PROTEIN 2B) (EXTRA ELEVEN-NINETEEN LEUKEMIA FUSION GENE) (EEN) (EEN FUSION PARTNER OF MLL). [SWISSPROT;Acc:Q99961] 0.215238121 SH3GL1
0.801332 2490 0.172887 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] 0.215749527 REXO4
0.80202 329 0.228764 L-MYC-1 PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P12524] 0.285234782 MYCL1
0.803133 1841 0.187564 60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 0.233540397 no value
1842 60S RIBOSOMAL PROTEIN L31. [SWISSPROT;Acc:P12947] RPL31
1843 40S RIBOSOMAL PROTEIN S19. [SWISSPROT;Acc:P39019] RPS19
0.804471 1346 0.197255 RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [RefSeq;Acc:NM_013401] 0.245198397 RAB3IL1
0.806892 1534 0.195279 IRON-RESPONSIVE ELEMENT BINDING PROTEIN 1 (IRE-BP 1) (IRON REGULATORY PROTEIN 1) (IRP1) (FERRITIN REPRESSOR PROTEIN) (ACONITATE HYDRATASE) (EC 4.2.1.3) (CITRATE HYDRO-LYASE) (ACONITASE). [SWISSPROT;Acc:P21399] 0.242013801 ACO1
0.807018 304 0.241123 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.298782679 no value
0.807248 3105 0.0744473 NEUROGENIC DIFFERENTIATION FACTOR 6 (NEUROD6) (MY051 PROTEIN). [SWISSPROT;Acc:Q96NK8] 0.092223579 NEUROD6
0.807611 3075 0.083343 TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106] 0.10319696 TOB2
0.807655 280 0.245451 "OLIGOPEPTIDE TRANSPORTER, SMALL INTESTINE ISOFORM (PEPTIDE TRANSPORTER 1) (INTESTINAL H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 1). [SWISSPROT;Acc:P46059]" 0.303905752 SLC15A1
0.808409 1682 0.192536 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] 0.238166572 NMNAT3
0.808504 2450 0.175357 0.216890702 HDHD3
2451 E-1 ENZYME. [RefSeq;Acc:NM_021204] ENOPH1
0.808729 922 0.208436 ALPHA CRYSTALLIN C CHAIN (SMALL STRESS PROTEIN-LIKE PROTEIN HSP22) (E2IG1) (PROTEIN KINASE H11). [SWISSPROT;Acc:Q9UJY1] 0.257732813 HSPB8
0.809316 2085 0.185296 RUVB-LIKE 1 (EC 3.6.1.-) (49-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (49 KDA TBP-INTERACTING PROTEIN) (TIP49A) (PONTIN 52) (NUCLEAR MATRIX PROTEIN 238) (NMP 238) (54 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-54) (TIP60-ASSOCIATED PROTEIN 54-ALPHA) 0.228953833 RUVBL1
0.809352 2897 0.141717 CELL DIVISION PROTEIN KINASE 2 (EC 2.7.1.-) (P33 PROTEIN KINASE). [SWISSPROT;Acc:P24941] 0.175099339 CDK2
0.81025 3204 0.000178236 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 0.000219977 no value
0.812069 3168 0.0509886 "RIBOSOMAL PROTEIN S6 KINASE, 52KDA, POLYPEPTIDE 1; RIBOSOMAL PROTEIN S6 KINASE, 52KD, POLYPEPTIDE 1. [RefSeq;Acc:NM_012424]" 0.062788507 RPS6KC1
0.81274 3104 0.0749538 CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 3 (CHD-3) (MI-2 AUTOANTIGEN 240 KDA PROTEIN) (MI2-ALPHA). [SWISSPROT;Acc:Q12873] 0.092223589 CHD3
0.812851 248 0.253658 PXR2B PROTEIN. [RefSeq;Acc:NM_016559] 0.312059652 PEX5L
0.812918 1193 0.202064 PROTEASOME SUBUNIT BETA TYPE 6 PRECURSOR (EC 3.4.25.1) (PROTEASOME DELTA CHAIN) (MACROPAIN DELTA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX DELTA CHAIN) (PROTEASOME SUBUNIT Y). [SWISSPROT;Acc:P28072] 0.248566276 PSMB6
0.813521 2284 0.180926 APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] 0.222398684 APOA1BP
0.814552 2834 0.157265 GK001 PROTEIN. [RefSeq;Acc:NM_020198] 0.193069319 CCDC47

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/