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 Hugo Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 186 to 235 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    93 MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence 88.2482 110.265 1.24949
    94 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Low confidence 247.087 228.693 1.08043
    95 MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence 88.2482 110.265 1.24949
    SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Low confidence 200.497 185.679 1.0798
    96 MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] High confidence 88.2482 110.265 1.24949
    SLC7A7 y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Low confidence 200.497 185.679 1.0798
    97 MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] High confidence 88.2482 110.265 1.24949
    SLC7A11 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 200.497 185.679 1.0798
    98 MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] High confidence 88.2482 110.265 1.24949
    SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 200.497 185.679 1.0798
    99 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 88.2482 110.265 1.24949
    EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence 200.497 185.679 1.0798
    100 MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] High confidence 88.2482 110.265 1.24949
    SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 200.497 185.679 1.0798
    101 MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] High confidence 88.2482 110.265 1.24949
    ROGDI leucine zipper domain protein. [refseq;acc:nm_024589] Low confidence 221.996 238.82 1.07579
    102 DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] 229.556 213.456 1.07543
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] High confidence 88.2482 110.265 1.24949
    103 PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence 203.948 189.652 1.07538
    TRO trophinin. [swissprot;acc:q12816] High confidence 88.2482 110.265 1.24949
    104 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Low confidence 219.277 204.212 1.07377
    HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 252.371 202.016 1.24926
    105 E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Low confidence 220.497 205.364 1.07369
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] High confidence 266.716 333.165 1.24914
    106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 252.329 202.004 1.24913
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Low confidence 220.497 205.364 1.07369
    107 FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] 227.429 211.97 1.07293
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] High confidence 252.309 201.998 1.24907
    108 DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Low confidence 197.731 212.069 1.07251
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 252.296 201.995 1.24902
    109 GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 266.933 333.281 1.24856
    NEURL neuralized-like. [refseq;acc:nm_004210] Low confidence 232.704 216.996 1.07239
    110 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 197.752 212.031 1.07221
    DTX2 deltex 2. [refseq;acc:nm_020892] High confidence 333.144 267.393 1.2459
    111 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 332.925 267.274 1.24563
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 203.914 190.189 1.07217
    112 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 197.762 212.013 1.07206
    PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] High confidence 332.874 267.246 1.24557
    113 CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Low confidence 197.763 212.011 1.07205
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 267.246 1.24557
    114 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] Low confidence 197.779 211.983 1.07182
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 332.874 267.246 1.24557
    115 DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Low confidence 197.779 211.983 1.07182
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 332.874 267.246 1.24557
    116 GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 268.565 334.483 1.24545
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 204.161 190.791 1.07008
    117 F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 226.395 211.713 1.06935
    NEURL neuralized-like. [refseq;acc:nm_004210] High confidence 332.326 266.948 1.24491
    118 NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 284.753 228.934 1.24382

    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/