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 Rank Gene measured description final Hugo
Results: HTML CSV LaTeX Showing element 1902 to 1951 of 3206 in total
expected
Rank
measured
description
final
Hugo
0.704322 2925 0.117871 0.167353852 NUP93
0.705791 1022 0.178897 0.25347022 TBC1D10B
0.70777 245 0.221131 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-2 SUBUNIT (AMPK GAMMA-2 CHAIN) (AMPK GAMMA2) (H91620P). [SWISSPROT;Acc:Q9UGJ0]" 0.312433418 PRKAG2
0.708531 138 0.248966 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-1 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q8N1C3] 0.351383355 GABRG1
0.709572 2733 0.145697 ADP-RIBOSYLATION FACTOR GTPASE ACTIVATING PROTEIN 1 (ADP-RIBOSYLATION FACTOR 1 GTPASE ACTIVATING PROTEIN) (ARF1 GAP) (ARF1-DIRECTED GTPASE- ACTIVATING PROTEIN) (GAP PROTEIN). [SWISSPROT;Acc:Q8N6T3] 0.205330819 ARFGAP1
0.710442 367 0.198738 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN F (HNRNP F). [SWISSPROT;Acc:P52597] 0.279738529 HNRPF
0.712692 2665 0.149127 ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [SWISSPROT;Acc:P14868] 0.209244667 DARS
0.712745 413 0.197804 0.27752422 CCDC49
0.713719 137 0.250789 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-2 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P18507] 0.351383388 GABRG2
0.715239 770 0.188365 HSP90 CO-CHAPERONE CDC37 (HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT) (P50CDC37). [SWISSPROT;Acc:Q16543] 0.26335952 CDC37
0.715904 2808 0.141529 PEROXISOMAL TARGETING SIGNAL 2 RECEPTOR (PTS2 RECEPTOR) (PEROXIN-7). [SWISSPROT;Acc:O00628] 0.197692707 PEX7
0.71709 2801 0.142496 TUMOR PROTEIN D53 (HD53) (D52-LIKE 1). [SWISSPROT;Acc:Q16890] 0.198714248 TPD52L1
0.717375 75 0.291345 MITOCHONDRIAL RIBOSOME RECYCLING FACTOR. [RefSeq;Acc:NM_138777] 0.406126503 MRRF
0.719698 2486 0.155588 CEREBRAL CELL ADHESION MOLECULE. [RefSeq;Acc:NM_016174] 0.216185122 CEECAM1
0.722002 701 0.191556 HRD1 PROTEIN ISOFORM A; SYNOVIOLIN1. [RefSeq;Acc:NM_032431] 0.265312284 SYVN1
0.722066 2244 0.16152 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) (PBG-D). [SWISSPROT;Acc:P08397] 0.223691463 HMBS
0.722847 1221 0.179279 VISININ-LIKE PROTEIN 3 (VILIP-3) (CALCIUM-BINDING PROTEIN BDR-1) (HLP2) (HIPPOCALCIN-LIKE PROTEIN 1). [SWISSPROT;Acc:P37235] 0.248017907 HPCAL1
0.725721 2434 0.157677 IMP2 INNER MITOCHONDRIAL MEMBRANE PROTEASE-LIKE; INNER MITOCHONDRIAL MEMBRANE PEPTIDASE 2 LIKE. [RefSeq;Acc:NM_032549] 0.217269447 IMMP2L
2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] no value
0.729107 747 0.192847 0.264497529 CLUAP1
0.729117 2895 0.127708 CELL DIVISION CONTROL PROTEIN 2 HOMOLOG (EC 2.7.1.-) (P34 PROTEIN KINASE) (CYCLIN-DEPENDENT KINASE 1) (CDK1). [SWISSPROT;Acc:P06493] 0.175154331 CDC2
0.729445 1033 0.184799 CATHEPSIN L PRECURSOR (EC 3.4.22.15) (MAJOR EXCRETED PROTEIN) (MEP). [SWISSPROT;Acc:P07711] 0.253341924 CTSL1
0.729447 2795 0.145818 SERINE/THREONINE-PROTEIN KINASE PAK 4 (EC 2.7.1.-) (P21-ACTIVATED KINASE 4) (PAK-4). [SWISSPROT;Acc:O96013] 0.199902118 PAK4
0.730041 1911 0.169445 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L27 (L27MT) (HSPC250). [SWISSPROT;Acc:Q9P0M9] 0.232103402 MRPL27
0.730409 2698 0.151787 ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [SWISSPROT;Acc:O75454] 0.207810966 no value
0.730667 1592 0.175549 LAMIN A/C (70 KDA LAMIN). [SWISSPROT;Acc:P02545] 0.240258558 LMNA
0.731277 1023 0.185352 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [SWISSPROT;Acc:Q9UBN4] 0.253463462 TRPC4
0.732966 2309 0.162756 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 1 SUBUNIT (MU-ADAPTIN 3A) (AP-3 ADAPTER COMPLEX MU3A SUBUNIT). [SWISSPROT;Acc:Q9Y2T2] 0.222051227 AP3M1
0.735452 2970 0.104104 0.141551046 RIBC2
0.735578 3197 0.027115 NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079] 0.036862168 VPS24
0.735941 2497 0.158519 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] 0.215396343 SH3GL2
0.737338 2066 0.16919 "60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL PRECURSOR (HSP60) (60 KDA CHAPERONIN) (CPN60) (HEAT SHOCK PROTEIN 60) (HSP-60) (MITOCHONDRIAL MATRIX PROTEIN P1) (P60 LYMPHOCYTE PROTEIN) (HUCHA60). [SWISSPROT;Acc:P10809]" 0.229460573 HSPD1
0.737404 1914 0.171101 DNA-DIRECTED RNA POLYMERASES III 39 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C39 SUBUNIT). [SWISSPROT;Acc:Q9H1D9] 0.232031559 POLR3F
0.738297 3065 0.0764589 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B LIGHT CHAIN 3 A). [SWISSPROT;Acc:Q9H492] 0.103561168 MAP1LC3A
0.740509 575 0.200205 BILE ACID COENZYME A: AMINO ACID N-ACYLTRANSFERASE; GLYCINE N-CHOLOYLTRANSFERASE. [RefSeq;Acc:NM_001701] 0.270361333 BAAT
0.741531 641 0.198895 LBP-9. [RefSeq;Acc:NM_014553] 0.268222097 TFCP2L1
0.742662 2420 0.162045 P300/CBP-ASSOCIATED FACTOR (EC 2.3.1.-) (P/CAF) (HISTONE ACETYLASE PCAF). [SWISSPROT;Acc:Q92831] 0.218194818 PCAF
0.742944 2968 0.106453 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 1 (RALGDS-LIKE 1). [SWISSPROT;Acc:Q9NZL6] 0.143285362 RGL1
0.743642 2115 0.16968 "4-AMINOBUTYRATE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.19) (GAMMA-AMINO-N-BUTYRATE TRANSAMINASE) (GABA TRANSAMINASE) (GABA AMINOTRANSFERASE) (GABA-AT) (GABA-T). [SWISSPROT;Acc:P80404]" 0.22817431 no value
0.74385 5 0.489705 "NADH-UBIQUINONE OXIDOREDUCTASE 18 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-18 KDA) (CI-18 KDA) (COMPLEX I- AQDQ) (CI-AQDQ). [SWISSPROT;Acc:O43181]" 0.658338375 NDUFS4
0.744637 899 0.193159 SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN (SRP68). [SWISSPROT;Acc:Q9UHB9] 0.259400218 SRP68
0.74486 3171 0.0439931 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN. [SWISSPROT;Acc:O94903] 0.05906224 PROSC
0.744947 324 0.214269 HIGH-MOBILITY GROUP 20A. [RefSeq;Acc:NM_018200] 0.287629858 HMG20A
0.749104 3009 0.09144 SEPTIN 7 (CDC10 PROTEIN HOMOLOG). [SWISSPROT;Acc:Q16181] 0.122065828 SEPT7
0.74967 1188 0.186417 TGF-BETA RECEPTOR TYPE I PRECURSOR (EC 2.7.1.37) (TGFR-1) (TGF-BETA TYPE I RECEPTOR) (SERINE/THREONINE-PROTEIN KINASE RECEPTOR R4) (SKR4) (ACTIVIN RECEPTOR-LIKE KINASE 5) (ALK-5). [SWISSPROT;Acc:P36897] 0.248665413 TGFBR1
0.749796 2145 0.170664 ANAPHASE PROMOTING COMPLEX SUBUNIT 11 (HEPATOCELLULAR CARCINOMA ASSOCIATED RING FINGER PROTEIN) (HSPC214). [SWISSPROT;Acc:Q9NYG5] 0.227613911 ANAPC11
0.750509 1377 0.18361 HOMEOBOX PROTEIN PRH (HEMATOPOIETICALLY EXPRESSED HOMEOBOX) (HOMEOBOX PROTEIN HEX). [SWISSPROT;Acc:Q03014] 0.244647299 HHEX
0.750535 2920 0.126707 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 3). [SWISSPROT;Acc:P47986] 0.16882224 no value
0.750817 2214 0.168935 "PININ, DESMOSOME ASSOCIATED PROTEIN; PININ. [RefSeq;Acc:NM_002687]" 0.225001565 PNN
0.751425 2914 0.130387 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 2). [SWISSPROT;Acc:P51669] 0.173519646 UBE2D2

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/