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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Hugo Rank Gene expected description final measured
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
Hugo  : no value
Rank
expected
description
final
measured
499 2.05361 SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 0.274221006 0.563143
504 0.104626 ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451] 0.274067631 0.0286746
508 0.493083 HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506] 0.273980243 0.135095
515 1.96129 ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1] 0.272423252 0.534301
522 2.5522 "PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]" 0.271974767 0.694134
534 0.14739 SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578] 0.271366443 0.0399967
542 0.561935 PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [RefSeq;Acc:NM_003981] 0.271077616 0.152328
554 0.136094 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 0.270999456 0.0368814
560 1.99055 ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576] 0.270867348 0.539175
582 0.351165 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 0.270031751 0.0948257
614 0.338281 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.26884454 0.090945
626 0.324228 0.268259065 0.0869771
633 0.454193 F-ACTIN CAPPING PROTEIN ALPHA-2 SUBUNIT (CAPZ ALPHA-2). [SWISSPROT;Acc:P47755] 0.268258207 0.121841
644 0.154846 0.268129626 0.0415188
647 1.47537 RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 0.268041237 0.39546
648 1.365 0.268001465 0.365822
654 0.423045 CYSTEINE-RICH PROTEIN 1 (CYSTEINE-RICH INTESTINAL PROTEIN) (CRIP) (CYSTEINE-RICH HEART PROTEIN) (HCRHP). [SWISSPROT;Acc:P50238] 0.267626375 0.113218
658 0.757899 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 1. [SWISSPROT;Acc:Q15695] 0.267251969 0.20255
659 0.106766 SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 0.267114063 0.0285187
672 0.163636 0.266704148 0.0436424
680 0.628521 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5 (EC 2.7.1.-) (MAPK/ERK KINASE KINASE 5) (MEK KINASE 5) (MEKK 5) (APOPTOSIS SIGNAL- REGULATING KINASE 1) (ASK-1). [SWISSPROT;Acc:Q99683] 0.265644266 0.166963
688 0.25292 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 0.265643682 0.0671866
698 0.159817 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] 0.265486775 0.0424293
703 0.540454 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 2 (WASP-FAMILY PROTEIN MEMBER 2) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 2). [SWISSPROT;Acc:Q9Y6W5] 0.26514745 0.1433
712 1.98825 HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] 0.264886206 0.52666
713 0.263425 DJ153G14.2 (POSSIBLE CA BINDING PROTEIN SIMILAR TO NEFA) (FRAGMENT). [SPTREMBL;Acc:Q9UJN8] 0.264880326 0.0697761
721 1.43987 DJ470L14.3 (NOVEL PROTEIN SIMILAR TO THE ARP2/3 PROTEIN COMPLEX SUBUNIT P21-ARC (ARC21)). [SPTREMBL;Acc:Q9H5B6] 0.264677367 0.381101
745 0.1121 BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 0.26449777 0.0296502
752 0.121579 LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [SWISSPROT;Acc:P50851] 0.264496336 0.0321572
768 1.32226 DPY-30-LIKE PROTEIN. [SWISSPROT;Acc:Q9C005] 0.263639526 0.3486
772 1.87133 CASEIN KINASE II BETA CHAIN (CK II) (PHOSVITIN) (G5A). [SWISSPROT;Acc:P13862] 0.263275852 0.492676
773 0.139602 "SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 0.263275598 0.0367538
777 0.216002 HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [SWISSPROT;Acc:O60229] 0.263226266 0.0568574
784 0.144194 0.26256363 0.0378601
787 1.38457 CBF1 INTERACTING COREPRESSOR. [RefSeq;Acc:NM_004882] 0.262184649 0.363013
810 0.450503 0.261549868 0.117829
811 0.118668 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 0.261549028 0.0310375
813 0.155406 DEAD-BOX PROTEIN ABSTRAKT HOMOLOG. [SWISSPROT;Acc:Q9UJV9] 0.261359922 0.0406169
820 0.0991465 "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 0.261326421 0.0259096
827 0.114163 PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 0.261276421 0.0298281
829 0.969143 PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1) (INOSINE PHOSPHORYLASE) (PNP). [SWISSPROT;Acc:P00491] 0.261099755 0.253043
847 0.157329 0.260622644 0.0410035
852 0.250194 KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] 0.260535025 0.0651843
878 0.15268 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 0.260106104 0.039713
909 0.619267 NEUROTRIMIN PRECURSOR (HNT). [SWISSPROT;Acc:Q9P121] 0.258219799 0.159907
924 0.1468 FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402] 0.257679837 0.0378274
936 0.28817 RHO INTERACTING PROTEIN 3. [RefSeq;Acc:NM_015134] 0.256707499 0.0739754
960 0.240043 "ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP" 0.256126611 0.0614814
980 1.26105 0.255279331 0.32192
985 0.454719 CYTOKINE-LIKE NUCLEAR FACTOR N-PAC. [RefSeq;Acc:NM_032569] 0.255168577 0.11603

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/