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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 751 to 800 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    751 u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] no value 223.463 212.875 1.04974
    752 step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7
    753 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] LBP 224.434 235.583 1.04968
    754 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] SPCS2
    755 uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] UMPS
    756 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] CLPTM1
    757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] BPI
    758 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] PLTP
    759 osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 231.809 243.289 1.04952
    760 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 246.055 234.458 1.04946
    761 signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB 213.325 203.303 1.0493
    762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 213.256 203.237
    763 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] N6AMT1 228.78 218.091 1.04901
    764 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] PRPF3 222.082 211.707
    765 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] HEMK1 229.045 218.343
    766 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] TRIOBP 213.804 224.226 1.04875
    767 rho interacting protein 3. [refseq;acc:nm_015134] no value 213.803 224.224 1.04874
    768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 210.946 221.225 1.04873
    769 cab2. [refseq;acc:nm_033419] PERLD1
    770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5
    771 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] DNAJB1
    772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] ETF1
    773 suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] VPS52
    774 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] MCFD2 225.996 215.535 1.04854
    775 histone deacetylase 2 (hd2). [swissprot;acc:q92769] no value 226.003 215.541
    776 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 225.996 215.535
    777 histone deacetylase 1 (hd1). [swissprot;acc:q13547] HDAC1 225.989 215.53 1.04853
    778 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] SNX6 209.191 219.332 1.04848
    779 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] DCTD 230.516 241.641 1.04826
    780 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] POLR2F 232.762 243.933 1.04799
    781 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] MRTO4 245.84 257.636 1.04798
    782 translin. [swissprot;acc:q15631] no value 224.385 235.131 1.04789
    783 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] TSNAX
    784 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] PQBP1
    785 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] NET1 244.447 233.508 1.04685
    786 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] ARHGEF3
    787 down-regulated in metastasis. [refseq;acc:nm_014503] UTP20
    788 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 138.705 132.538 1.04653
    789 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] no value 224.244 234.511 1.04578
    790 40s ribosomal protein s21. [swissprot;acc:p35265] RPS21
    791 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] SERPINB9
    792 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] no value
    793 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] SERPINB10
    794 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] SERPINB8
    795 serpin b11. [swissprot;acc:q96p15] no value
    796 placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] SERPINB6
    797 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] no value
    798 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] SERPINB1
    799 sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] SQSTM1 221.965 212.404 1.04501
    800 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] SCP2

    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/