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

    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/