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 Hugo description measured final
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
expected
Rank
Hugo
description
measured
final
0.059666 1813 CPB1 CARBOXYPEPTIDASE B PRECURSOR (EC 3.4.17.2) (PANCREAS-SPECIFIC PROTEIN) (PASP). [SWISSPROT;Acc:P15086] 0.0139875 0.234429994
0.0611788 2163 PLTP PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [SWISSPROT;Acc:P55058] 0.0139025 0.227243751
0.0622988 2157 BPIL2 0.0141571 0.227245148
0.0626341 2631 CHRNA6 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]" 0.0131531 0.209999026
0.0632961 2635 CHRNA3 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]" 0.0132921 0.20999872
0.063934 1619 OPHN1 OLIGOPHRENIN 1. [SWISSPROT;Acc:O60890] 0.0153184 0.239597084
0.0677865 2630 CHRNA2 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]" 0.0142351 0.209999041
0.0681463 1623 ARHGAP10 0.0163276 0.23959628
0.0691587 2160 LBP LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [SWISSPROT;Acc:P18428] 0.0157159 0.227244005
0.0703876 1733 SLC39A6 "LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" 0.0166846 0.23703891
0.0707964 1922 PCYT1B CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE B (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE B) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE B) (CT B) (CCT B) (CCT-BETA). [SWISSPROT;Acc:Q9Y5K3] 0.0164226 0.231969422
0.0715398 1809 CPA5 CARBOXYPEPTIDASE A5. [RefSeq;Acc:NM_080385] 0.0167711 0.234430345
0.0725001 2015 BCCIP BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [RefSeq;Acc:NM_016567] 0.0167203 0.230624509
0.0728736 2067 RAB26 RAS-RELATED PROTEIN RAB-26. [SWISSPROT;Acc:Q9ULW5] 0.016721 0.229452092
0.0742417 1727 GAD2 "GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q05329]" 0.0175982 0.237039292
0.0754368 1916 no value BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT 0.0174991 0.231970338
0.0797142 944 ABHD3 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 3; LUNG ALPHA/BETA HYDROLASE 3. [RefSeq;Acc:NM_138340] 0.0204392 0.25640601
0.0807026 1917 POR NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435] 0.0187206 0.231970222
1918 PAPSS1 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 1 (PAPS SYNTHETHASE 1) (PAPSS 1) (SULFURYLASE KINASE 1) (SK1) (SK 1) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT
1919 PCYT1A CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE A (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE A) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE A) (CT A) (CCT A) (CCT-ALPHA). [SWISSPROT;Acc:P49585]
0.081259 874 HECTD1 HECT DOMAIN CONTAINING PROTEIN 1 (FRAGMENT). [SWISSPROT;Acc:Q9ULT8] 0.0211489 0.260265324
0.08159 1466 MARK2 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 ISOFORM B; ELKL MOTIF KINASE 1; ELKL MOTIF KINASE. [RefSeq;Acc:NM_004954] 0.0198288 0.243029783
0.0821011 1950 ESF1 0.0189917 0.231320896
0.0826631 1992 HAS1 HYALURONAN SYNTHASE 1 (EC 2.4.1.212) (HYALURONATE SYNTHASE 1) (HYALURONIC ACID SYNTHASE 1) (HA SYNTHASE 1) (HUHAS1). [SWISSPROT;Acc:Q92839] 0.0190828 0.230850283
0.0842001 1961 SCAPER ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12] 0.0194686 0.231218253
0.0842002 1963 MED11 0.231217978
1964 PEX1 PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [SWISSPROT;Acc:O43933]
0.0845876 524 PYGM "GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]" 0.0229997 0.27190392
0.0847765 1907 LTV1 0.0196837 0.232183447
0.0850893 1622 ARHGAP26 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] 0.0203871 0.239596518
0.0851144 525 PYGB "GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]" 0.0231429 0.271903462
0.085173 1959 NUDT12 NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [RefSeq;Acc:NM_031438] 0.0196941 0.231224684
0.0860464 2013 PRMT3 PROTEIN ARGININE N-METHYLTRANSFERASE 3 (EC 2.1.1.-) (FRAGMENT). [SWISSPROT;Acc:O60678] 0.0198445 0.230625569
0.0865184 2159 BPI BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] 0.0196608 0.227244147
0.0865364 1462 MARK1 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1. [RefSeq;Acc:NM_018650] 0.021031 0.243030678
0.0870115 1437 AKT2 "RAC-BETA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-BETA) (PROTEIN KINASE AKT-2) (PROTEIN KINASE B, BETA) (PKB BETA). [SWISSPROT;Acc:P31751]" 0.0211896 0.24352643
0.0871461 2320 no value MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] 0.0193287 0.2217965
0.0875599 2326 SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.0194204 0.221795594
0.0881799 1993 HAS2 HYALURONAN SYNTHASE 2 (EC 2.4.1.212) (HYALURONATE SYNTHASE 2) (HYALURONIC ACID SYNTHASE 2) (HA SYNTHASE 2). [SWISSPROT;Acc:Q92819] 0.0203563 0.230849661
0.088691 2322 SERPINB10 BOMAPIN (PROTEASE INHIBITOR 10) (SERPIN B10). [SWISSPROT;Acc:P48595] 0.0196713 0.221795898
0.0887019 1540 no value DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 0.0214576 0.241906881
0.0888852 2632 CHRNA4 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]" 0.0186658 0.209998965
0.0892747 1083 ATP11A POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IH (EC 3.6.3.1) (ATPASE CLASS I TYPE 11A) (ATPASE IS). [SWISSPROT;Acc:P98196] 0.0225037 0.252072536
0.089649 1438 AKT1 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.0218319 0.24352642
0.0896565 2328 SERPINB8 PLASMINOGEN ACTIVATOR INHIBITOR-2 PRECURSOR (PAI-2) (PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR) (MONOCYTE ARG-SERPIN) (UROKINASE INHIBITOR). [SWISSPROT;Acc:P05120] 0.0198854 0.221795408
0.0899059 1732 GAD1 "GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q99259]" 0.0213112 0.237038949
0.0899599 2327 SERPINB6 PLACENTAL THROMBIN INHIBITOR (CYTOPLASMIC ANTIPROTEINASE) (CAP) (PROTEASE INHIBITOR 6) (PI-6). [SWISSPROT;Acc:P35237] 0.0199527 0.221795489
0.0900703 2324 no value CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 0.0199772 0.221795642
0.0901025 656 BAIAP3 BAI1-ASSOCIATED PROTEIN 3; BAI-ASSOCIATED PROTEIN 3. [RefSeq;Acc:NM_003933] 0.0241104 0.26758858
0.0901539 1730 NOSTRIN NOSTRIN. [RefSeq;Acc:NM_052946] 0.02137 0.237039108

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/