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 Hugo measured Rank description final
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
expected
Hugo
measured
Rank
description
final
0.059666 CPB1 0.0139875 1813 CARBOXYPEPTIDASE B PRECURSOR (EC 3.4.17.2) (PANCREAS-SPECIFIC PROTEIN) (PASP). [SWISSPROT;Acc:P15086] 0.234429994
0.0611788 PLTP 0.0139025 2163 PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [SWISSPROT;Acc:P55058] 0.227243751
0.0622988 BPIL2 0.0141571 2157 0.227245148
0.0626341 CHRNA6 0.0131531 2631 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]" 0.209999026
0.0632961 CHRNA3 0.0132921 2635 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]" 0.20999872
0.063934 OPHN1 0.0153184 1619 OLIGOPHRENIN 1. [SWISSPROT;Acc:O60890] 0.239597084
0.0677865 CHRNA2 0.0142351 2630 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]" 0.209999041
0.0681463 ARHGAP10 0.0163276 1623 0.23959628
0.0691587 LBP 0.0157159 2160 LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [SWISSPROT;Acc:P18428] 0.227244005
0.0703876 SLC39A6 0.0166846 1733 "LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" 0.23703891
0.0707964 PCYT1B 0.0164226 1922 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE B (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE B) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE B) (CT B) (CCT B) (CCT-BETA). [SWISSPROT;Acc:Q9Y5K3] 0.231969422
0.0715398 CPA5 0.0167711 1809 CARBOXYPEPTIDASE A5. [RefSeq;Acc:NM_080385] 0.234430345
0.0725001 BCCIP 0.0167203 2015 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] 0.230624509
0.0728736 RAB26 0.016721 2067 RAS-RELATED PROTEIN RAB-26. [SWISSPROT;Acc:Q9ULW5] 0.229452092
0.0742417 GAD2 0.0175982 1727 "GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q05329]" 0.237039292
0.0754368 no value 0.0174991 1916 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 0.231970338
0.0797142 ABHD3 0.0204392 944 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 3; LUNG ALPHA/BETA HYDROLASE 3. [RefSeq;Acc:NM_138340] 0.25640601
0.0807026 PAPSS1 0.0187206 1918 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 0.231970222
PCYT1A 1919 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE A (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE A) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE A) (CT A) (CCT A) (CCT-ALPHA). [SWISSPROT;Acc:P49585]
POR 1917 NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435]
0.081259 HECTD1 0.0211489 874 HECT DOMAIN CONTAINING PROTEIN 1 (FRAGMENT). [SWISSPROT;Acc:Q9ULT8] 0.260265324
0.08159 MARK2 0.0198288 1466 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 ISOFORM B; ELKL MOTIF KINASE 1; ELKL MOTIF KINASE. [RefSeq;Acc:NM_004954] 0.243029783
0.0821011 ESF1 0.0189917 1950 0.231320896
0.0826631 HAS1 0.0190828 1992 HYALURONAN SYNTHASE 1 (EC 2.4.1.212) (HYALURONATE SYNTHASE 1) (HYALURONIC ACID SYNTHASE 1) (HA SYNTHASE 1) (HUHAS1). [SWISSPROT;Acc:Q92839] 0.230850283
0.0842001 SCAPER 0.0194686 1961 ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12] 0.231218253
0.0842002 MED11 1963 0.231217978
PEX1 1964 PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [SWISSPROT;Acc:O43933]
0.0845876 PYGM 0.0229997 524 "GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]" 0.27190392
0.0847765 LTV1 0.0196837 1907 0.232183447
0.0850893 ARHGAP26 0.0203871 1622 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] 0.239596518
0.0851144 PYGB 0.0231429 525 "GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]" 0.271903462
0.085173 NUDT12 0.0196941 1959 NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [RefSeq;Acc:NM_031438] 0.231224684
0.0860464 PRMT3 0.0198445 2013 PROTEIN ARGININE N-METHYLTRANSFERASE 3 (EC 2.1.1.-) (FRAGMENT). [SWISSPROT;Acc:O60678] 0.230625569
0.0865184 BPI 0.0196608 2159 BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] 0.227244147
0.0865364 MARK1 0.021031 1462 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1. [RefSeq;Acc:NM_018650] 0.243030678
0.0870115 AKT2 0.0211896 1437 "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]" 0.24352643
0.0871461 no value 0.0193287 2320 MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] 0.2217965
0.0875599 0.0194204 2326 SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.221795594
0.0881799 HAS2 0.0203563 1993 HYALURONAN SYNTHASE 2 (EC 2.4.1.212) (HYALURONATE SYNTHASE 2) (HYALURONIC ACID SYNTHASE 2) (HA SYNTHASE 2). [SWISSPROT;Acc:Q92819] 0.230849661
0.088691 SERPINB10 0.0196713 2322 BOMAPIN (PROTEASE INHIBITOR 10) (SERPIN B10). [SWISSPROT;Acc:P48595] 0.221795898
0.0887019 no value 0.0214576 1540 DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 0.241906881
0.0888852 CHRNA4 0.0186658 2632 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]" 0.209998965
0.0892747 ATP11A 0.0225037 1083 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IH (EC 3.6.3.1) (ATPASE CLASS I TYPE 11A) (ATPASE IS). [SWISSPROT;Acc:P98196] 0.252072536
0.089649 AKT1 0.0218319 1438 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.24352642
0.0896565 SERPINB8 0.0198854 2328 PLASMINOGEN ACTIVATOR INHIBITOR-2 PRECURSOR (PAI-2) (PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR) (MONOCYTE ARG-SERPIN) (UROKINASE INHIBITOR). [SWISSPROT;Acc:P05120] 0.221795408
0.0899059 GAD1 0.0213112 1732 "GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q99259]" 0.237038949
0.0899599 SERPINB6 0.0199527 2327 PLACENTAL THROMBIN INHIBITOR (CYTOPLASMIC ANTIPROTEINASE) (CAP) (PROTEASE INHIBITOR 6) (PI-6). [SWISSPROT;Acc:P35237] 0.221795489
0.0900703 no value 0.0199772 2324 CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 0.221795642
0.0901025 BAIAP3 0.0241104 656 BAI1-ASSOCIATED PROTEIN 3; BAI-ASSOCIATED PROTEIN 3. [RefSeq;Acc:NM_003933] 0.26758858
0.0901539 no value 0.02137 1731 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/