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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measured Hugo Rank Gene description expected final
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
measured
Hugo
Rank
description
expected
final
0.0196608 BPI 2159 BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] 0.0865184 0.227244147
0.0196713 SERPINB10 2322 BOMAPIN (PROTEASE INHIBITOR 10) (SERPIN B10). [SWISSPROT;Acc:P48595] 0.088691 0.221795898
0.0196837 LTV1 1907 0.0847765 0.232183447
0.0196941 NUDT12 1959 NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [RefSeq;Acc:NM_031438] 0.085173 0.231224684
0.0197176 STARD13 2625 STAR-RELATED LIPID TRANSFER PROTEIN 13 (STARD13) (START DOMAIN- CONTAINING PROTEIN 13) (46H23.2). [SWISSPROT;Acc:Q9Y3M8] 0.0938936 0.209999404
0.0198288 MARK2 1466 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 ISOFORM B; ELKL MOTIF KINASE 1; ELKL MOTIF KINASE. [RefSeq;Acc:NM_004954] 0.08159 0.243029783
0.0198445 PRMT3 2013 PROTEIN ARGININE N-METHYLTRANSFERASE 3 (EC 2.1.1.-) (FRAGMENT). [SWISSPROT;Acc:O60678] 0.0860464 0.230625569
0.0198854 SERPINB8 2328 PLASMINOGEN ACTIVATOR INHIBITOR-2 PRECURSOR (PAI-2) (PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR) (MONOCYTE ARG-SERPIN) (UROKINASE INHIBITOR). [SWISSPROT;Acc:P05120] 0.0896565 0.221795408
0.0199527 SERPINB6 2327 PLACENTAL THROMBIN INHIBITOR (CYTOPLASMIC ANTIPROTEINASE) (CAP) (PROTEASE INHIBITOR 6) (PI-6). [SWISSPROT;Acc:P35237] 0.0899599 0.221795489
0.0199772 no value 2324 CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 0.0900703 0.221795642
0.0199967 BRP44 3010 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] 0.163819 0.122065817
0.0200176 HHATL 2598 0.0940277 0.212890457
0.0200935 SERPINB9 2321 CYTOPLASMIC ANTIPROTEINASE 3 (CAP3) (CAP-3) (PROTEASE INHIBITOR 9) (SERPIN B9). [SWISSPROT;Acc:P50453] 0.0905944 0.22179627
0.0202662 NFYA 3114 CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT B (CBF-B) (NF-Y PROTEIN CHAIN A) (NF-YA) (CAAT-BOX DNA BINDING PROTEIN SUBUNIT A). [SWISSPROT;Acc:P23511] 0.2235 0.09067651
0.0202703 no value 2773 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 0.100647 0.201399942
0.0203563 HAS2 1993 HYALURONAN SYNTHASE 2 (EC 2.4.1.212) (HYALURONATE SYNTHASE 2) (HYALURONIC ACID SYNTHASE 2) (HA SYNTHASE 2). [SWISSPROT;Acc:Q92819] 0.0881799 0.230849661
0.0203871 ARHGAP26 1622 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] 0.0850893 0.239596518
0.0204267 GLI3 2360 ZINC FINGER PROTEIN GLI3. [SWISSPROT;Acc:P10071] 0.0927234 0.220297142
0.0204392 ABHD3 944 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 3; LUNG ALPHA/BETA HYDROLASE 3. [RefSeq;Acc:NM_138340] 0.0797142 0.25640601
0.0206348 LYPLA2P1 2774 LYSOPHOSPHOLIPASE II; ACYL-PROTEIN THIOESTERASE. [RefSeq;Acc:NM_007260] 0.102457 0.201399612
0.0206788 CLPTM1 2162 CLEFT LIP AND PALATE ASSOCIATED TRANSMEMBRANE PROTEIN 1. [RefSeq;Acc:NM_001294] 0.0909983 0.227243806
0.0207502 HS3ST2 2991 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 2; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006043] 0.153323 0.135336512
0.0208556 RAB37 2068 RAS-RELATED PROTEIN RAB-37. [SWISSPROT;Acc:Q96AX2] 0.0908932 0.229451708
0.0209707 FAM86C 2543 0.0977138 0.214613494
0.0210051 HS3ST6 2995 C439A6.1 (NOVEL PROTEIN SIMILAR TO HEPARAN SULFATE (GLUCOSAMINE) 3-O- SULFOTRANSFERASES) (FRAGMENT). [SPTREMBL;Acc:Q96QI5] 0.155207 0.135336035
0.021031 MARK1 1462 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1. [RefSeq;Acc:NM_018650] 0.0865364 0.243030678
0.0210454 HS3ST4 2990 0.155504 0.135336712
0.0211489 HECTD1 874 HECT DOMAIN CONTAINING PROTEIN 1 (FRAGMENT). [SWISSPROT;Acc:Q9ULT8] 0.081259 0.260265324
0.0211896 AKT2 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]" 0.0870115 0.24352643
0.0213112 GAD1 1732 "GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q99259]" 0.0899059 0.237038949
0.02137 no value 1731 0.0901539 0.237039108
NOSTRIN 1730 NOSTRIN. [RefSeq;Acc:NM_052946]
0.0213901 CPA1 1810 CARBOXYPEPTIDASE A1 PRECURSOR (EC 3.4.17.1). [SWISSPROT;Acc:P15085] 0.0912429 0.234430295
0.0214423 SLC3A1 1812 "NEUTRAL AND BASIC AMINO ACID TRANSPORT PROTEIN RBAT (B(0,+)-TYPE AMINO ACID TRANSPORT PROTEIN) (NBAT) (D2H). [SWISSPROT;Acc:Q07837]" 0.0914656 0.234430212
0.0214512 TST 2641 THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1) (RHODANESE). [SWISSPROT;Acc:Q16762] 0.10215 0.209997063
0.0214576 no value 1540 DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 0.0887019 0.241906881
0.0215242 VAMP3 2735 VESICLE-ASSOCIATED MEMBRANE PROTEIN 3 (VAMP-3) (SYNAPTOBREVIN 3) (CELLUBREVIN) (CEB). [SWISSPROT;Acc:Q15836] 0.104827 0.205330688
0.0215869 RHOC 2636 TRANSFORMING PROTEIN RHOC (H9). [SWISSPROT;Acc:P08134] 0.102796 0.209997471
0.0217044 DDOST 2999 DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE--PROTEIN GLYCOSYLTRANSFERASE 48 KDA SUBUNIT PRECURSOR (EC 2.4.1.119) (OLIGOSACCHARYL TRANSFERASE 48 KDA SUBUNIT) (DDOST 48 KDA SUBUNIT). [SWISSPROT;Acc:P39656] 0.160664 0.135091869
0.0217565 no value 2541 0.101375 0.214614057
0.0218319 AKT1 1438 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.089649 0.24352642
0.0218584 ZC3H12C 2141 0.0959445 0.227823377
0.0221128 SDF2L1 1890 STROMAL CELL-DERIVED FACTOR 2-LIKE PROTEIN 1 PRECURSOR (SDF2 LIKE PROTEIN 1) (PWP1-INTERACTING PROTEIN 8). [SWISSPROT;Acc:Q9HCN8] 0.0950179 0.232722466
0.0222862 TBX19 2452 T-BOX TRANSCRIPTION FACTOR TBX19 (T-BOX PROTEIN 19). [SWISSPROT;Acc:O60806] 0.102768 0.216859334
0.0223215 HAS3 1991 HYALURONAN SYNTHASE 3 (EC 2.4.1.212) (HYALURONATE SYNTHASE 3) (HYALURONIC ACID SYNTHASE 3) (HA SYNTHASE 3). [SWISSPROT;Acc:O00219] 0.0966924 0.230850615
0.0223249 SLC25A13 2589 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR2 (SOLUTE CARRIER FAMILY 25, MEMBER 13) (CITRIN). [SWISSPROT;Acc:Q9UJS0]" 0.104865 0.212891813
0.0223435 ARHGEF3 1527 "RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3; RHOGEF PROTEIN; 59.8 KDA PROTEIN; EXCHANGE FACTOR FOUND IN PLATELETS AND LEUKEMIC AND NEURONAL TISSUES, XPLN. [RefSeq;Acc:NM_019555]" 0.0922076 0.242317336
0.0223509 CASP3 1829 APOPAIN PRECURSOR (EC 3.4.22.-) (CYSTEINE PROTEASE CPP32) (YAMA PROTEIN) (CPP-32) (CASPASE-3) (CASP-3) (SREBP CLEAVAGE ACTIVITY 1) (SCA-1). [SWISSPROT;Acc:P42574] 0.0954818 0.234085449
0.0224671 LIPM 1849 BA304I5.1 (NOVEL LIPASE) (FRAGMENT). [SPTREMBL;Acc:Q96LG2] 0.0962388 0.233451581
0.0224883 ALDH18A1 1681 DELTA 1-PYRROLINE-5-CARBOXYLATE SYNTHETASE (P5CS) [INCLUDES: GLUTAMATE 5-KINASE (EC 2.7.2.11) (GAMMA-GLUTAMYL KINASE) (GK); GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41) (GLUTAMATE-5-SEMIALDEHYDE DEHYDROGENASE) (GLUTAMYL-GAMMA-SEMIALDEHYDE DEHYDR 0.0944225 0.238166751

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/