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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1325 to 1374 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    166 MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted High confidence 55.6495 65.1458 1.17064
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 209.299 249.187 1.19058
    SLC16A3 monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Measured Low confidence 10325 11178.2 1.08263
    UBE1C ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Rooted 72.46 77.3071 1.06689
    167 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared High confidence 173408 242989 1.40126
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Low confidence 23804.2 26534 1.11468
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Ranked High confidence 209.299 249.187 1.19058
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Measured 23693.7 18263 1.29736
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Low confidence 12376.5 11436.5 1.08219
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Rooted High confidence 55.65 65.1448 1.17062
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Ranked Low confidence 212.695 201.131 1.05749
    Rooted 68.0417 72.5283 1.06594
    168 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked High confidence 82.5916 98.0548 1.18722
    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] Measured Low confidence 12376.4 11436.5 1.08218
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 23693.7 18263 1.29736
    ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Rooted Low confidence 72.4531 77.213 1.0657
    FER proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Ranked 216.796 205.073 1.05717
    HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared High confidence 173408 242989 1.40126
    RNF20 ring finger protein 20. [refseq;acc:nm_019592] Low confidence 53551.4 48045.1 1.11461
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Rooted High confidence 56.3709 65.8949 1.16895
    169 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Low confidence 72.4389 77.1711 1.06533
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Ranked High confidence 82.5916 98.0548 1.18722
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 53.7761 1.1671
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured 23693.7 18263 1.29736
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Low confidence 12375.5 11435.8 1.08217
    RBM10 rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Squared 67930.9 60946.6 1.1146
    RPL29 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Ranked 216.79 205.07 1.05715
    SYMPK symplekin. [swissprot;acc:q92797] Squared High confidence 124118 88668.8 1.39979
    170 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Measured Low confidence 6131.26 6633.65 1.08194
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted High confidence 53.4993 45.9227 1.16499
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared 96730.5 69286.7 1.39609
    FES proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Ranked Low confidence 216.783 205.066 1.05714
    INADL inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] Squared 67882.7 60913.7 1.11441
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured High confidence 23693.7 18263 1.29736
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted Low confidence 70.7428 75.3259 1.06479
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked High confidence 227.199 192.715 1.17894
    171 CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared 96602.7 69211.2 1.39577
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Low confidence 219.889 208.064 1.05683
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted High confidence 61.6639 71.7355 1.16333
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Measured 23693.7 18263 1.29736
    MPDZ multiple pdz domain protein. [refseq;acc:nm_003829] Squared Low confidence 67876.4 60909.3 1.11438
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 96.9641 103.242 1.06474
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Measured 7012.61 7584.69 1.08158
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked High confidence 227.202 192.823 1.17829
    172 CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Low confidence 213.671 202.205 1.0567
    CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared High confidence 121579 87259.3 1.39331
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Measured Low confidence 7012.61 7584.69 1.08158
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted High confidence 56.7592 65.9889 1.16261
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Ranked 174.667 205.556 1.17685
    TRO trophinin. [swissprot;acc:q12816] Measured 23693.7 18263 1.29736

    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/