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 network_comparison red green
    Results: HTML CSV LaTeX Showing element 2175 to 2224 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		network_comparison
    		red
    		green
    2175 PSMD2 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 1.00671 210.209 208.808
    2176 PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] 1.00669 218.089 216.64
    2177 PXMP2 peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 1.00667 210.961 209.563
    2178 HSPA2 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
    2179 no value heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]
    2180 HSPA8 heat shock cognate 71 kda protein. [swissprot;acc:p11142]
    2181 CALR calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 1.00664 227.117 225.62
    2182 PEO1 twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] 218.062 216.624
    2183 RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]
    2184 SUPV3L1 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] 1.00663 211.713 210.318
    2185 BAG1 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
    2186 GSK3A glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]
    2187 GSK3B glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]
    2188 P4HB protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 1.00662 209.54 208.162
    2189 HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]
    2190 ZFPL1 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]
    2191 HUS1 hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507]
    2192 HABP4 hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
    2193 P4HA1 prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674]
    2194 PROX1 homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]
    2195 RAD1 rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853]
    2196 P4HA2 prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460]
    2197 COQ6 ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] 1.00659 193.787 195.064
    2198 KMO kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
    2199 SQLE squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]
    2200 ISL2 insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] 1.00656 196.748 195.466
    2201 NSFL1C p47 protein isoform a. [refseq;acc:nm_016143] 1.00654 213.642 212.254
    2202 TSG101 tumor susceptibility gene 101 protein. [swissprot;acc:q99816] 1.00652 195.97 194.7
    2203 SYMPK symplekin. [swissprot;acc:q92797] 1.00651 162.741 163.8
    2204 RUVBL2 ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] 1.00649 219.377 220.8
    2205 no value 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 1.00645 199.129 200.413
    2206 VCP transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] 215.571 214.19
    2207 SAP30 sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] 199.129 200.413
    2208 AP2M1 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]
    2209 ABCC10 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]
    2210 MAN2B1 lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]
    2211 RRN3 rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]
    2212 MRPS16 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 1.00643 224.411 225.854
    2213 DHDH dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 1.00642 210.127 211.475
    2214 FABP4 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] 1.00637 221.509 220.108
    2215 no value fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469]
    2216 FABP7 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]
    2217 WDR4 wd-repeat protein 4. [swissprot;acc:p57081]
    2218 PMP2 myelin p2 protein. [swissprot;acc:p02689]
    2219 KLHL8 kelch-like protein 8. [swissprot;acc:q9p2g9]
    2220 PNMT phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
    2221 no value beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
    2222 BCMO1 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]
    2223 FABP3 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]
    2224 RPE65 retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]

    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/