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 red Hugo Network Comparison Type Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1330 to 1379 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		red
    		Hugo
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    167 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 12376.5 PSCD2 Measured Low confidence 11436.5 1.08219
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 209.299 GAD1 Ranked High confidence 249.187 1.19058
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 173408 no value Squared 242989 1.40126
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 55.65 RAB24 Rooted 65.1448 1.17062
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 23693.7 MAGEA4 Measured 18263 1.29736
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 68.0417 RHOBTB2 Rooted Low confidence 72.5283 1.06594
    212.695 Ranked 201.131 1.05749
    168 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 72.4531 ARRB2 Rooted 77.213 1.0657
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 82.5916 no value 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] 216.796 FER Ranked Low confidence 205.073 1.05717
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 173408 HSD17B14 Squared High confidence 242989 1.40126
    ring finger protein 20. [refseq;acc:nm_019592] 53551.4 RNF20 Low confidence 48045.1 1.11461
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 56.3709 SNRPD3 Rooted High confidence 65.8949 1.16895
    169 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 216.79 RPL29 Ranked Low confidence 205.07 1.05715
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] 82.5916 ATG3 High confidence 98.0548 1.18722
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 72.4389 ARRB1 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] 62.762 COPS3 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] 12375.5 PSCD3 Measured Low confidence 11435.8 1.08217
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 23693.7 MAGEA10 High confidence 18263 1.29736
    rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] 67930.9 RBM10 Squared Low confidence 60946.6 1.1146
    symplekin. [swissprot;acc:q92797] 124118 SYMPK 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] 6131.26 APBA1 Measured Low confidence 6633.65 1.08194
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 53.4993 B9D1 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] 96730.5 CTPS2 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] 67882.7 INADL 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] 23693.7 MAGEB4 Measured High confidence 18263 1.29736
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 TIA1 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] 70.7428 SLC15A1 Rooted Low confidence 75.3259 1.06479
    proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 216.783 FES Ranked 205.066 1.05714
    171 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 96602.7 CTPS Squared High confidence 69211.2 1.39577
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 219.889 FOXP3 Ranked Low confidence 208.064 1.05683
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 96.9641 NFU1 Rooted 103.242 1.06474
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 61.6639 LASS2 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] 23693.7 MAGED2 Measured 18263 1.29736
    multiple pdz domain protein. [refseq;acc:nm_003829] 67876.4 MPDZ Squared Low confidence 60909.3 1.11438
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 227.202 TIAL1 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] 7012.61 SENP8 Measured Low confidence 7584.69 1.08158
    172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 TIPRL Ranked High confidence 205.556 1.17685
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 213.671 CAPZA1 Low confidence 202.205 1.0567
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 121579 CSTF2T Squared High confidence 87259.3 1.39331
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 65.0717 UNC84A 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] 56.7592 SF3B1 High confidence 65.9889 1.16261
    trophinin. [swissprot;acc:q12816] 23693.7 TRO Measured 18263 1.29736
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] 7012.61 NEDD8 Low confidence 7584.69 1.08158
    ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] 67872.2 WBP11 Squared 60906.5 1.11437
    173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 145.551 MRPS17 Rooted High confidence 168.796 1.1597
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 BCAR3 Measured 5940.64 1.29727
    elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] 67872.2 ELAC2 Squared Low confidence 60906.5 1.11437

    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/