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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Gene expected measured Rank final description Hugo
Results: HTML CSV LaTeX Showing element 1402 to 1451 of 3206 in total
expected
measured
Rank
final
description
Hugo
0.449228 0.109553 1426 0.243869483 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] MAPRE1
1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] SLC39A7
0.450013 0.0937258 2690 0.208273539 SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [SWISSPROT;Acc:O00422] SAP18
0.450503 0.117829 810 0.261549868 no value
0.450566 0.122154 536 0.271112334 BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059] BRD3
0.450769 0.10685 1725 0.23703937 VPS25
1726 CHMP6
0.451047 0.114013 1048 0.252774101 ANNEXIN A11 (ANNEXIN XI) (CALCYCLIN-ASSOCIATED ANNEXIN 50) (CAP-50) (56 KDA AUTOANTIGEN). [SWISSPROT;Acc:P50995] ANXA11
0.451392 0.113583 1089 0.251628296 RSPH10B
0.451492 0.114355 1042 0.25328245 "ATP-DEPENDENT DNA HELICASE II, 80 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P86) (KU86) (KU80) (86 KDA SUBUNIT OF KU ANTIGEN) (THYROID- LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 85 KDA SUBUNIT) (CTCBF) (CTC85) (NUCLEAR FACTOR IV) (DNA-REPAIR PROTE" XRCC5
0.452001 0.12174 590 0.269335687 5'-METHYLTHIOADENOSINE PHOSPHORYLASE (EC 2.4.2.28) (MTA PHOSPHORYLASE) (MTAPASE). [SWISSPROT;Acc:Q13126] MTAP
591 PUTATIVE RIBOSOMAL RNA METHYLTRANSFERASE 1 (EC 2.1.1.-) (RRNA (URIDINE-2'-O-)-METHYLTRANSFERASE) (JM23 PROTEIN). [SWISSPROT;Acc:Q9UET6] FTSJ1
0.452071 0.0451789 3080 0.09993762 MAST CELL CARBOXYPEPTIDASE A PRECURSOR (EC 3.4.17.1) (MC-CPA) (CARBOXYPEPTIDASE A3). [SWISSPROT;Acc:P15088] CPA3
0.452567 0.098396 2432 0.217417532 THNSL1
0.452671 0.115392 998 0.254913613 NUAK2
0.452838 0.112521 1197 0.248479589 SYNTAXIN 10 (SYN10). [SWISSPROT;Acc:O60499] STX10
0.453066 0.0943663 2688 0.208283782 EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [SWISSPROT;Acc:Q9H223] EHD4
0.453153 0.104281 2043 0.230123159 HUNTINGTIN INTERACTING PROTEIN 1 (HIP-I). [SWISSPROT;Acc:O00291] HIP1
0.453668 0.118571 812 0.261360731 NKAP
0.454193 0.121841 633 0.268258207 F-ACTIN CAPPING PROTEIN ALPHA-2 SUBUNIT (CAPZ ALPHA-2). [SWISSPROT;Acc:P47755] no value
0.45456 0.114033 1109 0.250864572 "PROPIONYL-COA CARBOXYLASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.4.1.3) (PCCASE BETA SUBUNIT) (PROPANOYL-COA:CARBON DIOXIDE LIGASE BETA SUBUNIT). [SWISSPROT;Acc:P05166]" PCCB
0.454692 0.0963713 2606 0.211948528 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE (EC 1.1.1.34) (HMG-COA REDUCTASE). [SWISSPROT;Acc:P04035] HMGCR
0.454719 0.11603 985 0.255168577 CYTOKINE-LIKE NUCLEAR FACTOR N-PAC. [RefSeq;Acc:NM_032569] no value
0.454799 0.122515 588 0.269382738 40S RIBOSOMAL PROTEIN S8. [SWISSPROT;Acc:P09058] RPS8
0.454991 0.0454705 3081 0.099937142 CARBOXYPEPTIDASE B PRECURSOR. [RefSeq;Acc:NM_020361] CPA6
0.455193 0.111932 1293 0.245900091 C22orf23
0.456048 0.107954 1752 0.236716311 SECRETORY PATHWAY COMPONENT SEC31B-1. [RefSeq;Acc:NM_015490] SEC31B
0.456524 0.113931 1163 0.249561907 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT (SIGMA-ADAPTIN 1A) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1A SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1A SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1A SMALL CHAIN) (CLATHRIN COAT ASSEMBLY PROT AP1S1
0.457513 0.144083 234 0.31492657 FOS-RELATED ANTIGEN 1 (FRA-1). [SWISSPROT;Acc:P15407] FOSL1
0.457652 0.107427 1798 0.234735126 "FOLYLPOLYGLUTAMATE SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 6.3.2.17) (FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE) (FPGS). [SWISSPROT;Acc:Q05932]" FPGS
0.458992 0.147132 216 0.320554607 SORTING NEXIN 13 (RGS DOMAIN- AND PHOX DOMAIN-CONTAINING PROTEIN) (RGS-PX1). [SWISSPROT;Acc:Q9Y5W8] SNX13
0.45954 0.122728 664 0.267067067 BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 (BARD-1). [SWISSPROT;Acc:Q99728] BARD1
0.459557 0.107268 1860 0.233416094 POLR3GL
0.459899 0.120499 800 0.262011877 SYNTAXIN 1B. [SWISSPROT;Acc:Q15531] STX1B
0.459981 0.111297 1537 0.241959994 "INHIBITOR OF GROWTH FAMILY, MEMBER 1; INHIBITOR OF GROWTH 1. [RefSeq;Acc:NM_005537]" ING1
0.460002 0.110811 1579 0.240892431 OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [SWISSPROT;Acc:Q13133] NR1H3
0.460314 0.119625 893 0.259876954 RHO-GTPASE-ACTIVATING PROTEIN 1 (GTPASE-ACTIVATING PROTEIN RHOOGAP) (RHO-RELATED SMALL GTPASE PROTEIN ACTIVATOR) (CDC42 GTPASE-ACTIVATING PROTEIN) (P50-RHOGAP). [SWISSPROT;Acc:Q07960] ARHGAP1
0.460606 0.0485629 3059 0.105432626 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]" GNAI2
0.460869 0.100955 2399 0.219053571 WILLIAMS BEUREN SYNDROME CRITICAL REGION 20A ISOFORM 2; NOL1/NOP2/SUN GENE FAMILY MEMBER; WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY A; WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20. [RefSeq;Acc:NM_018044] NSUN5
2400 NSUN2
0.460892 0.117727 973 0.255432943 G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG (GTP-BINDING PROTEIN GST1-HS). [SWISSPROT;Acc:P15170] GSPT1
0.461922 0.110487 1635 0.239189733 INOSITOL-1(OR 4)-MONOPHOSPHATASE (EC 3.1.3.25) (IMPASE) (IMP) (INOSITOL MONOPHOSPHATASE) (LITHIUM-SENSITIVE MYO-INOSITOL MONOPHOSPHATASE A1). [SWISSPROT;Acc:P29218] IMPA1
0.461933 0.112103 1504 0.24268238 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [SWISSPROT;Acc:P25388] no value
0.462009 0.126731 477 0.27430418 OVARIAN CARCINOMA IMMUNOREACTIVE ANTIGEN. [RefSeq;Acc:NM_017830] OCIAD1
0.462821 0.162688 129 0.351513868 DELTEX 2. [RefSeq;Acc:NM_020892] DTX2
0.463351 0.107843 1886 0.232745802 J DOMAIN PROTEIN C21ORF55. [SWISSPROT;Acc:Q9NX36] C21orf55
0.464305 0.116454 1118 0.250813582 PARAFIBROMIN. [RefSeq;Acc:NM_024529] CDC73
0.464479 0.116498 1117 0.250814353 PAF1
0.464538 0.124556 645 0.268128764 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22) (UDP-GLC DEHYDROGENASE) (UDP-GLCDH) (UDPGDH). [SWISSPROT;Acc:O60701] UGDH
0.464548 0.116452 1125 0.250678078 ADHESION REGULATING MOLECULE 1 PRECURSOR (110 KDA CELL MEMBRANE GLYCOPROTEIN) (GP110). [SWISSPROT;Acc:Q16186] ADRM1

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/