MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis
Session lost

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.
  • Resetting the view coordinate localhost/Mk5/AffectedProteins/

    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 1 to 50 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    1 UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 24 2.4
    2 no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec (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 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 HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 322 1.49767
    8 HBS1L hbs1-like. [refseq;acc:nm_006620]
    9 XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 309 1.45755
    10 ATPBD1C protein x 0004. [refseq;acc:nm_016301]
    11 RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] 337 232 1.45259
    12 RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
    13 UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 212.554 1.3585
    14 ATG4A 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 MAP1LC3B 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 MAP1LC3A 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 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 75.447 1.32866
    18 GBE1 1,4-alpha-glucan branching enzyme (ec (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 245.247 1.32082
    19 PYGB glycogen phosphorylase, brain form (ec [swissprot;acc:p11216]
    20 PYGL glycogen phosphorylase, liver form (ec [swissprot;acc:p06737]
    21 MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
    22 PYGM glycogen phosphorylase, muscle form (ec (myophosphorylase). [swissprot;acc:p11217]
    23 MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 44 1.31818
    24 PANK1 pantothenate kinase 1 (ec (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
    25 PANK2 pantothenate kinase 2, mitochondrial precursor (ec (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
    26 PANK3 pantothenate kinase 3 (ec (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
    27 SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305]
    28 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 153.671 1.31416
    29 PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 243.678 1.29991
    30 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] 187.457
    31 PPP2R2B 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] 187.458 243.677 1.2999
    32 PPP2R2C 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] 187.462 243.673 1.29985
    33 PPP2R1B 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] 188.688 242.742 1.28647
    34 PPP2R1A 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] 189.07 242.453 1.28235
    35 NFYC 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] 260.532 204.309 1.27519
    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 PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 322 253 1.27273
    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 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 204.641 160.957 1.2714
    43 no value jun dimerization protein. [refseq;acc:nm_130469]
    44 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] 161.046 1.2707
    45 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 161.051 1.27066
    46 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 204.642 161.068 1.27053
    47 TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] 325.586 256.492 1.26938
    48 GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 65.4586 83.0461 1.26868
    49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 133 105 1.26667
    50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]

    - 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.