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 Gene Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 56024 to 56073 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		Value Type
    		description
    		red
    		network_comparison
    		green
    3775 Subtracted TBCA Measured tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347] 8199.38 193.34 8392.72
    3776 Divided no value rho interacting protein 3. [refseq;acc:nm_015134] 7855.02 1.02421 8045.18
    DDIT4L Squared similar to smhs1 protein. [refseq;acc:nm_145244] 48866.7 1.03038 47426.1
    FIGNL1 Ranked fidgetin-like 1. [refseq;acc:nm_022116] 201.671 1.01335 199.015
    PRKCQ Rooted protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759] 72.1591 1.02879 74.2368
    Subtracted NPEPPS Squared puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] 45814.5 1310 44504.5
    RABIF Rooted guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224] 70.7282 2.0663 72.7945
    SH2B2 Measured adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979] 8199.38 193.34 8392.72
    SMO Ranked smoothened homolog precursor (smo) (gx protein). [swissprot;acc:q99835] 203.027 2.671 200.356
    3777 Divided LETM1 Rooted leucine zipper-ef-hand containing transmembrane protein 1. [refseq;acc:nm_012318] 70.7548 1.02878 72.7914
    RPS13 Ranked 40s ribosomal protein s13. [swissprot;acc:q02546] 201.886 1.01335 199.227
    TRIOBP Measured protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 7855.01 1.02421 8045.19
    XPR1 Squared xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] 42122.1 1.03038 40880.3
    Subtracted MPHOSPH10 Ranked u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 202.91 2.668 200.242
    PRDX2 Measured peroxiredoxin 2 (ec 1.11.1.-) (thioredoxin peroxidase 1) (thioredoxin- dependent peroxide reductase 1) (thiol-specific antioxidant protein) (tsa) (prp) (natural killer cell enhancing factor b) (nkef-b). [swissprot;acc:p32119] 8283.53 193.23 8476.76
    STAT3 Rooted signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] 69.4573 2.0657 71.523
    TOP3A Squared dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 45807.8 1309.1 44498.7
    3778 Divided FOXA3 Rooted hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] 70.6106 1.02877 72.642
    FTMT Ranked mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 204.043 1.01334 201.357
    ORMDL3 Measured orm1-like 3. [refseq;acc:nm_139280] 7798.1 1.02419 7986.71
    SF3A2 Squared splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 44431.4 1.03038 43121.3
    Subtracted no value Measured ubiquitin and ribosomal protein s27a precursor; ubiquitin carboxyl extension protein 80; 40s ribosomal protein s27a; ubiquitin; ubiquitin-cep80. [refseq;acc:nm_002954] 8100.14 193.22 8293.36
    LMAN1 Squared ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257] 44221.8 1308.8 42913
    STAT4 Rooted signal transducer and activator of transcription 4. [swissprot;acc:q14765] 69.4572 2.0657 71.5229
    STAU1 Ranked double-stranded rna-binding protein staufen homolog. [swissprot;acc:o95793] 204.866 2.668 202.198
    3779 Divided ASPSCR1 alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083] 200.614 1.01334 197.974
    FKBP8 Measured 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 8396.92 1.02419 8198.63
    GNAS Rooted guanine nucleotide-binding protein g(s), alpha subunit (adenylate cyclase-stimulating g alpha protein). [swissprot;acc:p04895] 72.1311 1.02877 74.2061
    KLF5 Squared krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] 44431.4 1.03038 43121.3
    Subtracted C11orf54 Measured ptd012 protein. [refseq;acc:nm_014039] 8100.23 193.18 8293.41
    ERCC2 Squared tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] 45152.4 1308.2 43844.2
    SLC4A4 Ranked solute carrier family 4, sodium bicarbonate cotransporter, member 4; sodium bicarbonate cotransporter 1 (sodium bicarbonate cotransporter, kidney; sodium bicarbonate cotransporter, pancreas); solute carrier family 4, sodium bicarbonate cotransporter, member 5. [refseq;acc:nm_003759] 204.917 2.668 202.249
    STAT1 Rooted signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] 69.4571 2.0657 71.5228
    3780 Divided no value Squared dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 45694 1.03037 44347.3
    ACAA1 Measured 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 8168.73 1.02419 8366.35
    CREBL2 Ranked camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 200.614 1.01334 197.974
    MRPS30 Rooted mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92] 72.4004 1.02876 74.4823
    Subtracted IFRD1 Squared interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] 43239.2 1307.5 41931.7
    MAB21L2 Measured mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439] 8100.23 193.18 8293.41
    SLC20A2 Rooted solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] 70.6358 2.0641 72.6999
    STAU2 Ranked staufen homolog 2; staufen (drosophila, rna-binding protein) 2; staufen (drosophila, rna-binding protein) homolog 2. [refseq;acc:nm_014393] 204.866 2.668 202.198
    3781 Divided no value Measured proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] 7963.77 1.02418 8156.34
    Squared t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283] 45694 1.03037 44347.3
    ILF2 Rooted interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515] 72.2706 1.02875 74.3485
    RALB Ranked ras-related protein ral-b. [swissprot;acc:p11234] 201.947 1.01333 199.29
    Subtracted AGXT2L1 alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279] 199.247 2.666 196.581
    AXIN2 Rooted axin 2 (axis inhibition protein 2) (conductin) (axin-like protein) (axil). [swissprot;acc:q9y2t1] 71.2917 2.0632 73.3549
    MAB21L1 Measured mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584] 8100.23 193.18 8293.41
    RARS2 Squared arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 46272.9 1307.1 44965.8
    3782 Divided GFPT2 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] 46005.4 1.03037 44649.6

    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/