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 description Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1325 to 1374 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    166 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 23693.7 Measured High confidence 18263 1.29736
    monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] SLC16A3 10325 Low confidence 11178.2 1.08263
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 37094.3 Squared 41487.9 1.11844
    ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] UBE1C 72.46 Rooted 77.3071 1.06689
    167 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 23804.2 Squared 26534 1.11468
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 12376.5 Measured 11436.5 1.08219
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 209.299 Ranked High confidence 249.187 1.19058
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value 173408 Squared 242989 1.40126
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 55.65 Rooted 65.1448 1.17062
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 23693.7 Measured 18263 1.29736
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 68.0417 Rooted Low confidence 72.5283 1.06594
    212.695 Ranked 201.131 1.05749
    168 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 72.4531 Rooted 77.213 1.0657
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value 82.5916 Ranked High confidence 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] 12376.4 Measured Low confidence 11436.5 1.08218
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 23693.7 High confidence 18263 1.29736
    proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] FER 216.796 Ranked Low confidence 205.073 1.05717
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 173408 Squared High confidence 242989 1.40126
    ring finger protein 20. [refseq;acc:nm_019592] RNF20 53551.4 Low confidence 48045.1 1.11461
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 56.3709 Rooted High confidence 65.8949 1.16895
    169 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] RPL29 216.79 Ranked Low confidence 205.07 1.05715
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 82.5916 High confidence 98.0548 1.18722
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 72.4389 Rooted Low confidence 77.1711 1.06533
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 62.762 High confidence 53.7761 1.1671
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 12375.5 Measured Low confidence 11435.8 1.08217
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 23693.7 High confidence 18263 1.29736
    rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] RBM10 67930.9 Squared Low confidence 60946.6 1.1146
    symplekin. [swissprot;acc:q92797] SYMPK 124118 High confidence 88668.8 1.39979
    170 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] APBA1 6131.26 Measured Low confidence 6633.65 1.08194
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 53.4993 Rooted High confidence 45.9227 1.16499
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 96730.5 Squared 69286.7 1.39609
    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] INADL 67882.7 Low confidence 60913.7 1.11441
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 23693.7 Measured High confidence 18263 1.29736
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 227.199 Ranked 192.715 1.17894
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 70.7428 Rooted Low confidence 75.3259 1.06479
    proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] FES 216.783 Ranked 205.066 1.05714
    171 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS 96602.7 Squared High confidence 69211.2 1.39577
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 219.889 Ranked Low confidence 208.064 1.05683
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 96.9641 Rooted 103.242 1.06474
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 61.6639 High confidence 71.7355 1.16333
    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] MAGED2 23693.7 Measured 18263 1.29736
    multiple pdz domain protein. [refseq;acc:nm_003829] MPDZ 67876.4 Squared Low confidence 60909.3 1.11438
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 227.202 Ranked High confidence 192.823 1.17829
    sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] SENP8 7012.61 Measured Low confidence 7584.69 1.08158
    172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL 174.667 Ranked High confidence 205.556 1.17685
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 213.671 Low confidence 202.205 1.0567
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T 121579 Squared High confidence 87259.3 1.39331
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A 65.0717 Rooted Low confidence 69.26 1.06436
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 56.7592 High confidence 65.9889 1.16261
    trophinin. [swissprot;acc:q12816] TRO 23693.7 Measured 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/