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 Network Comparison Type green red Value Type Hugo network_comparison Interaction Map Filtered Gene description
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		green
    		red
    		Hugo
    		network_comparison
    		description
    1 24 10 UBAC1 2.4 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]
    2 28 15 no value 1.86667 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]
    3 PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
    4 PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
    5 PSCD4 cytohesin 4. [swissprot;acc:q9uia0]
    6 PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
    7 322 215 HLX 1.49767 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]
    8 HBS1L hbs1-like. [refseq;acc:nm_006620]
    9 309 212 XAB1 1.45755 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]
    10 ATPBD1C protein x 0004. [refseq;acc:nm_016301]
    11 232 337 RINT1 1.45259 rad50-interacting protein 1. [refseq;acc:nm_021930]
    12 RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
    13 212.554 288.754 UFC1 1.3585 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]
    14 75.3531 56.6768 ATG4A 1.32952 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]
    15 75.3948 56.7244 MAP1LC3B 1.32914 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]
    16 75.3954 56.7252 MAP1LC3A 1.32913 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]
    17 75.447 56.7841 ATG4B 1.32866 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]
    18 245.247 185.678 GBE1 1.32082 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]
    19 PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]
    20 PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]
    21 MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
    22 PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
    23 44 58 MRPS17 1.31818 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]
    24 PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
    25 PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
    26 PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
    27 SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305]
    28 153.671 201.949 ATF3 1.31416 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]
    29 243.678 187.458 PPP2R2D 1.29991 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]
    30 187.457 no value serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]
    31 243.677 187.458 PPP2R2B 1.2999 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]
    32 243.673 187.462 PPP2R2C 1.29985 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]
    33 242.742 188.688 PPP2R1B 1.28647 serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]
    34 242.453 189.07 PPP2R1A 1.28235 serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]
    35 204.309 260.532 NFYC 1.27519 nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]
    36 NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]
    37 253 322 PPP1R14A 1.27273 protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]
    38 MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
    39 PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
    40 FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
    41 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
    42 160.957 204.641 FOS 1.2714 proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]
    43 no value jun dimerization protein. [refseq;acc:nm_130469]
    44 161.046 FOSL2 1.2707 fos-related antigen 2. [swissprot;acc:p15408]
    45 161.051 FOSB 1.27066 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]
    46 161.068 204.642 FOSL1 1.27053 fos-related antigen 1 (fra-1). [swissprot;acc:p15407]
    47 256.492 325.586 TMEM132A 1.26938 gbp protein isoform a. [refseq;acc:nm_017870]
    48 83.0461 65.4586 GABARAP 1.26868 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]
    49 105 133 ARRB2 1.26667 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]
    50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]

    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/