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 1951 to 2000 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    488 SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Ranked 225.026 209.798 1.07258
    SCAMP1 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Squared 26866.1 32333.2 1.20349
    489 CDS2 phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] 26859 32321.2 1.20337
    MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Rooted 50.5505 46.2797 1.09228
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Ranked 231.276 215.627 1.07257
    PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Measured 5281.11 6044.61 1.14457
    490 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Ranked 220.183 236.015 1.0719
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Squared 5301.97 6377.93 1.20294
    NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Rooted 50.5505 46.2797 1.09228
    PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured 15274.9 13346.9 1.14445
    491 FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Squared 5302.25 6378.24 1.20293
    GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Ranked 251.83 234.951 1.07184
    NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Measured 5980.15 6843.48 1.14437
    PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Rooted 55.1759 60.2621 1.09218
    492 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Squared 5313 6389.9 1.20269
    NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured 5979.94 6842.76 1.14429
    PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Ranked 220.171 235.979 1.0718
    493 no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Rooted 55.1759 60.2621 1.09218
    AGXT serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Squared 28408.7 34148.5 1.20204
    COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked 220.172 235.98 1.0718
    NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Measured 5979.95 6842.78 1.14429
    494 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 5979.93 6842.72 1.14428
    ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 1.20082
    PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked 220.172 235.98 1.0718
    PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Rooted 55.1759 60.2621 1.09218
    495 CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Measured 10804.7 12363.6 1.14428
    PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Ranked 220.171 235.979 1.0718
    PARD6G partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared 30286.5 36362 1.2006
    RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Rooted 55.1759 60.2621 1.09218
    496 HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]
    NOSTRIN nostrin. [refseq;acc:nm_052946] Measured 4682.87 4093.05 1.1441
    PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Ranked 250.938 234.134 1.07177
    TUB tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 36362 1.2006
    497 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Ranked 251.344 234.514 1.07177
    HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Rooted 55.1759 60.2621 1.09218
    PRKCI protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Squared 30286.5 36362 1.2006
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] Measured 4682.87 4093.05 1.1441
    498 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Ranked 220.161 235.95 1.07172
    DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Rooted 55.1759 60.2621 1.09218
    NUMB numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 36362 1.2006
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Measured 4682.87 4093.05 1.1441
    499 GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
    TBC1D5 tbc1 domain family member 5. [swissprot;acc:q92609] Squared 30286.5 36362 1.2006
    TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] Rooted 55.1759 60.2621 1.09218
    TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Ranked 231.496 248.048 1.0715
    500 no value 60s ribosomal protein l7. [swissprot;acc:p18124] Rooted 52.6483 48.2135 1.09198
    ING2 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Ranked 224.662 240.673 1.07127
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Measured 4682.87 4093.05 1.1441
    TULP1 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Squared 30286.5 36362 1.2006

    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/