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 measured Rank Gene description expected final
Results: HTML CSV LaTeX Showing element 2258 to 2307 of 3206 in total
Hugo
measured
Rank
description
expected
final
PPM1B 0.138619 1178 PROTEIN PHOSPHATASE 2C BETA ISOFORM (EC 3.1.3.16) (PP2C-BETA). [SWISSPROT;Acc:O75688] 0.556039 0.249297262
PPP1CA 0.634044 2333 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-ALPHA 1 CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1A). [SWISSPROT;Acc:P08129] 2.86607 0.221224185
PPP1CC 0.518333 2393 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1G). [SWISSPROT;Acc:P36873] 2.36093 0.219546111
PPP1R12A 0.253813 529 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]" 0.933978 0.271754795
PPP1R12B 0.309836 528 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [RefSeq;Acc:NM_002481]" 1.13987 0.271816962
PPP1R13B 0.0795635 2197 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 13B; APOPTOSIS-STIMULATING PROTEIN OF P53, 1. [RefSeq;Acc:NM_015316]" 0.352238 0.225879945
PPP1R14A 0.0241928 3188 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14A; 17-KDA PKC-POTENTIATED INHIBITORY PROTEIN OF PP1. [RefSeq;Acc:NM_033256]" 0.648338 0.037315104
PPP1R14D 0.0229678 3190 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]" 0.615511 0.037315011
PPP1R2 0.0820717 2342 PROTEIN PHOSPHATASE INHIBITOR 2 (IPP-2). [SWISSPROT;Acc:P41236] 0.371844 0.220715408
PPP1R2P9 0.0612127 2340 TYPE 1 PROTEIN PHOSPHATASE INHIBITOR. [RefSeq;Acc:NM_025210] 0.27731 0.220737442
PPP1R7 0.0699506 2851 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 7; SDS22. [RefSeq;Acc:NM_002712]" 0.365592 0.19133515
PPP1R8 0.179673 1665 "NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE-1 (NIPP-1) (PROTEIN PHOSPHATASE 1, REGULATORY INHIBITOR SUBUNIT 8) [INCLUDES: ACTIVATOR OF RNA DECAY (EC 3.1.4.-) (ARD-1)]. [SWISSPROT;Acc:Q12972]" 0.752395 0.238801427
PPP2CA 0.517007 1827 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (PP2A-ALPHA) (REPLICATION PROTEIN C) (RP-C). [SWISSPROT;Acc:P05323]" 2.20733 0.234222794
PPP2R1A 0.1722 565 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, ALPHA ISOFORM (PP2A, SUBUNIT A, PR65-ALPHA ISOFORM) (PP2A, SUBUNIT A, R1-ALPHA ISOFORM) (MEDIUM TUMOR ANTIGEN-ASSOCIATED 61 KDA PROTEIN). [SWISSPROT;Acc:P30153]" 0.635895 0.270799424
PPP2R1B 0.181797 573 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, BETA ISOFORM (PP2A, SUBUNIT A, PR65-BETA ISOFORM) (PP2A, SUBUNIT A, R1-BETA ISOFORM). [SWISSPROT;Acc:P30154]" 0.671805 0.270609775
PPP2R2B 0.0961987 584 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, BETA ISOFORM (PP2A, SUBUNIT B, B-BETA ISOFORM) (PP2A, SUBUNIT B, B55- BETA ISOFORM) (PP2A, SUBUNIT B, PR55-BETA ISOFORM) (PP2A, SUBUNIT B, R2-BETA ISOFORM). [SWISSPROT;Acc:Q00005" 0.356254 0.270028407
PPP2R2C 0.101295 585 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, GAMMA ISOFORM (PP2A, SUBUNIT B, B-GAMMA ISOFORM) (PP2A, SUBUNIT B, B55-GAMMA ISOFORM) (PP2A, SUBUNIT B, PR55-GAMMA ISOFORM) (PP2A, SUBUNIT B, R2-GAMMA ISOFORM) (IMYPNO1). [SWISSP" 0.375141 0.270018473
PPP2R2D 0.0951162 583 UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR CELLS PROTEIN MDS026. [SPTREMBL;Acc:Q9NZ48] 0.352242 0.270030831
PPP2R5A 0.057253 2952 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, ALPHA ISOFORM (PP2A, B SUBUNIT, B' ALPHA ISOFORM) (PP2A, B SUBUNIT, B56 ALPHA ISOFORM) (PP2A, B SUBUNIT, PR61 ALPHA ISOFORM) (PP2A, B SUBUNIT, R5 ALPHA ISOFORM). [SWISSPROT;Acc:Q15" 0.387696 0.147674982
PPP2R5E 0.0735334 2953 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, EPSILON ISOFORM (PP2A, B SUBUNIT, B' EPSILON ISOFORM) (PP2A, B SUBUNIT, B56 EPSILON ISOFORM) (PP2A, B SUBUNIT, PR61 EPSILON ISOFORM) (PP2A, B SUBUNIT, R5 EPSILON ISOFORM). [SWISSPR" 0.497941 0.147674925
PPP3CA 0.283215 620 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, ALPHA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:Q08209]" 1.05458 0.268557151
PPP3CB 0.232385 618 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, BETA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, BETA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P16299]" 0.865296 0.268561278
PPP3CC 0.221484 617 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, GAMMA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, GAMMA ISOFORM) (CALCINEURIN, TESTIS-SPECIFIC CATALYTIC SUBUNIT) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P48454]" 0.824699 0.26856344
PPP4C 0.161804 1598 SERINE/THREONINE PROTEIN PHOSPHATASE 4 (EC 3.1.3.16) (PP4) (PROTEIN PHOSPHATASE X) (PP-X). [SWISSPROT;Acc:P33172] 0.67395 0.240083092
PPP6C 0.0987657 2760 SERINE/THREONINE PROTEIN PHOSPHATASE 6 (EC 3.1.3.16) (PP6). [SWISSPROT;Acc:O00743] 0.487402 0.202637043
PPT1 0.0690966 795 PALMITOYL-PROTEIN THIOESTERASE 1 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 1). [SWISSPROT;Acc:P50897] 0.263715 0.2620124
PQBP1 0.0312503 1602 POLYGLUTAMINE BINDING PROTEIN 1; NUCLEAR PROTEIN CONTAINING WW DOMAIN 38 KD. [RefSeq;Acc:NM_005710] 0.130205 0.240008448
PRAF2 0.0815544 2915 JM4 PROTEIN. [RefSeq;Acc:NM_007213] 0.470177 0.173454678
PRAM1 0.2316 1016 PRAM-1 PROTEIN; PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECULE-1. [RefSeq;Acc:NM_032152] 0.91233 0.253855513
PRB4 0.0770791 1449 SALIVARY PROLINE-RICH PROTEIN PO (ALLELE K) [CONTAINS: PEPTIDE P-D] (FRAGMENT). [SWISSPROT;Acc:P10162] 0.316634 0.243432796
PRDX4 0.0946713 328 PEROXIREDOXIN 4 (EC 1.11.1.-) (PRX-IV) (THIOREDOXIN PEROXIDASE AO372) (THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE A0372) (ANTIOXIDANT ENZYME AOE372) (AOE37-2). [SWISSPROT;Acc:Q13162] 0.331704 0.285408979
PRDX5 0.0637963 1910 "PEROXIREDOXIN 5, MITOCHONDRIAL PRECURSOR (PRX-V) (PEROXISOMAL ANTIOXIDANT ENZYME) (PLP) (THIOREDOXIN PEROXIDASE PMP20) (ANTIOXIDANT ENZYME B166) (AOEB166) (TPX TYPE VI) (LIVER TISSUE 2D-PAGE SPOT 71B) (ALU CO-REPRESSOR 1) (SBBI10). [SWISSPROT;Acc:P" 0.274826 0.232133423
PRKAA1 0.547661 240 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-1 CHAIN (EC 2.7.1.-) (AMPK ALPHA-1 CHAIN). [SWISSPROT;Acc:Q13131]" 1.75288 0.312434964
PRKAA2 0.630538 244 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-2 CHAIN (EC 2.7.1.-) (AMPK ALPHA-2 CHAIN). [SWISSPROT;Acc:P54646]" 2.01815 0.312433664
PRKAB1 0.355846 246 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-1 SUBUNIT (AMPK BETA-1 CHAIN) (AMPKB). [SWISSPROT;Acc:Q9Y478]" 1.13895 0.312433382
PRKAB2 0.404521 241 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-2 SUBUNIT (AMPK BETA-2 CHAIN). [SWISSPROT;Acc:O43741]" 1.29474 0.312434157
PRKACA 0.210706 1628 "CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]" 0.880269 0.239365467
PRKACB 1627 "CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]"
PRKACG 0.190544 1626 "CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" 0.796037 0.239365758
PRKAG1 0.180475 242 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA-1 CHAIN) (AMPKG). [SWISSPROT;Acc:P54619]" 0.577642 0.312433999
PRKAG2 0.221131 245 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-2 SUBUNIT (AMPK GAMMA-2 CHAIN) (AMPK GAMMA2) (H91620P). [SWISSPROT;Acc:Q9UGJ0]" 0.70777 0.312433418
PRKAG3 0.177169 243 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-3 SUBUNIT (AMPK GAMMA-3 CHAIN) (AMPK GAMMA3). [SWISSPROT;Acc:Q9UGI9]" 0.567061 0.312433759
PRKAR2A 0.392337 1629 CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [SWISSPROT;Acc:P13861] 1.63914 0.239355394
PRKAR2B 0.337407 1624 CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] 1.40952 0.239377235
PRKCE 0.0653647 2104 "PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]" 0.286244 0.228353083
PRKCH 0.0507599 2106 "PROTEIN KINASE C, ETA TYPE (EC 2.7.1.-) (NPKC-ETA) (PKC-L). [SWISSPROT;Acc:P24723]" 0.222289 0.228350931
PRKCI 0.086385 2648 "PROTEIN KINASE C, IOTA TYPE (EC 2.7.1.37) (NPKC-IOTA) (ATYPICAL PROTEIN KINASE C-LAMDA/IOTA) (APKC-LAMBDA/IOTA). [SWISSPROT;Acc:P41743]" 0.411431 0.209962302
PRKCZ 0.0704817 2645 "PROTEIN KINASE C, ZETA TYPE (EC 2.7.1.37) (NPKC-ZETA). [SWISSPROT;Acc:Q05513]" 0.335687 0.209962554
PRKRAP1 0.189161 1102 "PROTEIN KINASE, INTERFERON-INDUCIBLE DOUBLE STRANDED RNA DEPENDENT ACTIVATOR; PROTEIN ACTIVATOR OF THE INTERFERON-INDUCED PROTEIN KINASE. [RefSeq;Acc:NM_003690]" 0.753541 0.251029473
PRKX 0.143332 1625 PROTEIN KINASE PKX1 (EC 2.7.1.-). [SWISSPROT;Acc:P51817] 0.598798 0.239366197

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/