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 [...,...].
    description Rank Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1713 to 1762 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108] 3150 CRISP3 High confidence 0.00001 0.00001 1
    cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] 97 SLC7A11 Low confidence 200.497 185.679 1.0798
    cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 1880 CDA High confidence 220.852 223.225 1.01074
    3252 Low confidence 200.267 197.148 1.01582
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 1757 CTPS2 High confidence 180.537 178.325 1.0124
    4631 Low confidence 198.337 197.028 1.00664
    cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] 252 CYBB 210.414 201.035 1.04665
    cytochrome b5 outer mitochondrial membrane isoform precursor. [swissprot;acc:o43169] 3614 CYB5B 201.988 199.144 1.01428
    cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 1335 CYB5R1 200.614 196.269 1.02214
    1862 High confidence 210.856 213.147 1.01087
    cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1113 CYB5R2 Low confidence 200.326 195.686 1.02371
    1861 High confidence 210.856 213.147 1.01087
    cytochrome b5. [swissprot;acc:p00167] 3679 CYB5A Low confidence 202.099 199.338 1.01385
    cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 1365 COX11 198.57 194.297 1.02199
    1511 High confidence 213.268 209.509 1.01794
    cytochrome c oxidase copper chaperone. [swissprot;acc:q14061] 2658 COX17 Low confidence 200.053 196.574 1.0177
    cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674] 2378 COX5A 201.741 198.068 1.01854
    2791 High confidence 0.00001 0.00001 1
    cytochrome c oxidase polypeptide vb, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p10606] 4624 COX5B Low confidence 204.312 202.947 1.00673
    cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854] 3009 COX6B1 High confidence 0.00001 0.00001 1
    3229 Low confidence 201.768 198.603 1.01594
    cytochrome c oxidase polypeptide viia-heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-h) (cox viia-m). [swissprot;acc:p24310] 2871 COX7A1 204.066 200.634 1.01711
    cytochrome c oxidase polypeptide viia-liver/heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-l) (viial). [swissprot;acc:p14406] 2875 COX7A2
    cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] 4457 COX7C 204.713 202.839 1.00924
    cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 828 COX4I1 204.206 199.02 1.02606
    2402 High confidence 182.4 183.083 1.00374
    cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 868 COX4I2 Low confidence 204.037 198.928 1.02568
    2403 High confidence 182.4 183.083 1.00374
    cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397] 2877 no value Low confidence 204.066 200.634 1.01711
    cytochrome c oxidase subunit viia-related protein, mitochondrial precursor (cox7a-related protein) (eb1). [swissprot;acc:o14548] 2880 COX7A2L 200.635 1.0171
    cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 1369 HCCS High confidence 228.644 223.736 1.02194
    3221 Low confidence 200.125 196.981 1.01596
    cytochrome c. [swissprot;acc:p00001] 1533 CYCS High confidence 228.419 232.376 1.01732
    3810 Low confidence 201.347 198.714 1.01325
    cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 201 CYC1 208.591 219.23 1.051
    501 High confidence 238.704 255.68 1.07112
    cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 417 OXA1L Low confidence 211.182 203.991 1.03525
    1332 High confidence 220.681 215.78 1.02271
    cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 27 CYP24A1 Low confidence 284.798 237.743 1.19792
    3211 High confidence 0.00001 0.00001 1
    cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 26 CYP27A1 Low confidence 286.347 238.454 1.20085
    2977 High confidence 0.00001 0.00001 1
    cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 1258 CYP2D6 219.354 224.7 1.02437
    1270 Low confidence 201.858 197.415 1.02251
    cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] 678 CYP3A4 203.747 198.152 1.02824
    cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] 669 CYP3A43 203.712 198.082 1.02842
    cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] 675 CYP3A5 203.702 198.095 1.0283
    cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] 672 CYP3A7 203.727 198.116 1.02832
    cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 449 CYP4A11 203.077 196.283 1.03461
    1280 High confidence 218.368 213.22 1.02414

    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/