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

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/