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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2758 to 2807 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    690 CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Squared 33104 38818.5 1.17262
    PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Measured 6920.69 7747.63 1.11949
    SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Ranked 220.593 208.987 1.05553
    691 BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 217.602 206.195 1.05532
    CPN1 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Squared 33104 38818.5 1.17262
    KCNA2 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Rooted 63.1365 67.8053 1.07395
    PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Measured 6920.69 7747.63 1.11949
    692 CDC5L cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Ranked 217.602 206.195 1.05532
    CPZ cpz gene product. [refseq;acc:nm_003652] Squared 33104 38818.5 1.17262
    EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Rooted 51.3598 55.1508 1.07381
    PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Measured 6920.69 7747.63 1.11949
    693 CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Squared 33104 38818.5 1.17262
    EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Rooted 51.3598 55.1508 1.07381
    NOVA1 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Ranked 222.554 234.847 1.05524
    RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Measured 7725.1 8647.74 1.11943
    694 CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Squared 33104 38818.5 1.17262
    HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Measured 7725.1 8647.74 1.11943
    POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Ranked 241.907 229.35 1.05475
    PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Rooted 68.4526 73.4852 1.07352
    695 HIVEP1 zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Measured 7725.1 8647.74 1.11943
    KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Rooted 63.17 67.8116 1.07348
    PPIL4 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Ranked 226.135 214.405 1.05471
    SGPL1 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Squared 22778.5 26693.1 1.17186
    696 no value 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]
    HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Measured 7725.1 8647.74 1.11943
    PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Rooted 68.433 73.4502 1.07332
    SFRS18 sr rich protein. [refseq;acc:nm_032870] Ranked 225.293 213.64 1.05455
    697 FTH1 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 220.444 209.113 1.05419
    KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Rooted 63.1944 67.8162 1.07314
    OAT ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Squared 22778.5 26693.1 1.17186
    SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Measured 7105.27 7953.71 1.11941
    698 ACP1 red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Squared 17850.2 20913.9 1.17163
    ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Measured 7101.95 7949.85 1.11939
    CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Rooted 128.909 120.173 1.0727
    FTMT mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Ranked 220.437 209.118 1.05413
    699 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Rooted 57.0263 61.1552 1.0724
    CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked 220.438 209.118 1.05413
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Squared 18148.6 21253.1 1.17106
    HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Measured 7101.94 7949.84 1.11939
    700 no value 40s ribosomal protein s28. [swissprot;acc:p25112] 7161.14 8015.92 1.11936
    ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Rooted 57.0263 61.1552 1.0724
    dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Ranked 220.438 209.118 1.05413
    LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Squared 19072.5 22327.5 1.17066
    701 ATP6V0D2 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 25852.2 30258.6 1.17045
    CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured 7802.31 8731.82 1.11913
    DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Ranked 220.438 209.118 1.05413
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Rooted 51.4945 48.0189 1.07238
    702 AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked 220.438 209.118 1.05413
    ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Squared 25114 29386 1.1701
    RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Rooted 51.4945 48.0189 1.07238

    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 HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/