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 [...,...].
    Value Type Rank Filtered description Gene Network Comparison Type Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3730 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    Filtered
    description
    red
    green
    network_comparison
    1 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 4294 15915 3.70633
    1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 24 2.4
    2 0 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 14977 2.55362
    1 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 15 28 1.86667
    3 0 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 2.47638
    1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 15 28 1.86667
    4 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 21883 2.45711
    1 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15 28 1.86667
    5 0 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 11965.7 2.17144
    1 cytohesin 4. [swissprot;acc:q9uia0] 15 28 1.86667
    6 0 ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 15339.2 2.03897
    1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 28 1.86667
    7 0 cab2. [refseq;acc:nm_033419] 21866 10950 1.99689
    1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 322 1.49767
    8 0 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525 21888 1.89918
    1 hbs1-like. [refseq;acc:nm_006620] 215 322 1.49767
    9 0 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525 21888 1.89918
    1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 309 1.45755
    10 0 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 7509.39 14178.1 1.88805
    1 protein x 0004. [refseq;acc:nm_016301] 212 309 1.45755
    11 0 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 11627 6248 1.86092
    1 rad50-interacting protein 1. [refseq;acc:nm_021930] 337 232 1.45259
    12 0 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 9429.18 5208.84 1.81023
    1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 232 1.45259
    13 0 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 5210.5 9264.5 1.77804
    1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 212.554 1.3585
    14 0 dystrophin. [swissprot;acc:p11532] 10232.5 18054.8 1.76446
    1 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 75.3531 1.32952
    15 0 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] 19403 11267 1.72211
    1 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 56.7244 75.3948 1.32914
    16 0 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 1.69839
    1 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 56.7252 75.3954 1.32913
    17 0 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 6812 1.69451
    1 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 75.447 1.32866
    18 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 22286 13216 1.68629
    1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 245.247 1.32082
    19 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 22286 13216 1.68629
    1 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 185.678 245.247 1.32082
    20 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 22286 13216 1.68629
    1 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 185.678 245.247 1.32082
    21 0 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 6313.38 10621.4 1.68236
    1 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 185.678 245.247 1.32082
    22 0 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 20989 12479 1.68195
    1 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 185.678 245.247 1.32082
    23 0 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 15520.4 9285.44 1.67148
    1 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 44 1.31818
    24 0 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 13730.5 8257 1.66289
    1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 58 44 1.31818
    25 0 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 13730.5 8257 1.66289
    1 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 58 44 1.31818

    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
    - 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/