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 2651 to 2700 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    2651 NFKBIE nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] 201.37 201.594 1.00111
    2652 NFKB1 nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] 201.451 201.673 1.0011
    2653 NFKBIB nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] 201.452 201.674
    2654 NFKB2 nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]
    2655 BCL3 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] 201.445 201.667
    2656 FUBP1 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 217.179 216.943 1.00109
    2657 DLG2 channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 216.934 216.7 1.00108
    2658 DLG4 presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] 216.933
    2659 DLG3 presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]
    2660 DLG1 presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] 216.937 216.704
    2661 FES proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 204.768 204.549 1.00107
    2662 MOCS2 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]
    2663 ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]
    2664 RPL29 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]
    2665 FER proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]
    2666 TXNDC1 thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] 210.136 209.911
    2667 MOCS3 molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] 204.768 204.549
    2668 FUBP3 fuse binding protein 3 (fragment). [sptrembl;acc:q92946] 217.176 216.944
    2669 GPD1 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 214.575 214.354 1.00103
    2670 KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 144.391 144.538 1.00102
    2671 GNPNAT1 similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] 216.288 216.067
    2672 BCAT1 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 210.957 210.741
    2673 RAD9A rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] 216.372 216.588 1.001
    2674 GLUL glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 203.151 202.948
    2675 MRPS26 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 214.893 215.108
    2676 ERH enhancer of rudimentary homolog. [swissprot;acc:q14259]
    2677 SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 144.412 144.553 1.00098
    2678 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 144.411 144.552
    2679 ANAPC2 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 190.142 189.959 1.00096
    2680 HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 144.422 144.56
    2681 OTUB2 ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] 203.592 203.787
    2682 no value transforming protein n-ras. [swissprot;acc:p01111] 144.427 144.564 1.00095
    2683 YBX1 nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] 208.438 208.635
    2684 CSDA dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
    2685 YBX2 germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]
    2686 PSMB7 proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] 219.829 219.629 1.00091
    2687 BCAT2 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 210.939 210.755 1.00087
    2688 no value peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 194.557 194.392 1.00085
    2689 ACLY atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 213.792 213.619 1.00081
    2690 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 188.191 188.046 1.00077
    2691 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 188.193 188.048
    2692 AQP5 aquaporin 5. [swissprot;acc:p55064] 188.192
    2693 MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 188.193 188.049
    2694 AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 188.223 188.081 1.00075
    2695 SRP54 signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] 215.545 215.384
    2696 ACO1 iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] 201.652 201.794 1.0007
    2697 ARPC2 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 225.081 225.232 1.00067
    2698 SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 188.435 188.31 1.00066
    2699 CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985]
    2700 no value succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]

    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/