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 [...,...].
    description Gene Rank Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2251 to 2300 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] 1523 no value 219.306 223.179 1.01766
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 127 CHMP2A 94 114 1.21277
    putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] 2272 FMO6P 216.622 215.436 1.00551
    putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 396 no value 240.801 262.34 1.08945
    putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 2020 KIAA0664 223.168 221.176 1.00901
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 UBAC1 10 24 2.4
    putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] 1884 OLA1 215.081 217.373 1.01066
    putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1723 NADK 212.36 215.147 1.01312
    putative membrane protein. [refseq;acc:nm_019026] 2935 TMCO1 0.00001 0.00001 1
    putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [refseq;acc:nm_031212] 2891 SLC25A28
    putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 763 N6AMT1 228.78 218.091 1.04901
    putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80] 3146 DERL3 0.00001 0.00001 1
    putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 1793 NME2P1 193.1 190.823 1.01193
    putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 1231 PGAM4 212.724 207.637 1.0245
    putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 568 no value 226.3 212.38 1.06554
    putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 537 DHX15 229.803 215.301 1.06736
    putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] 1771 FTSJ1 223.016 225.734 1.01219
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 155 RBM15 249.663 298.263 1.19466
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 1572 RBM7 221.128 224.767 1.01646
    putative sialoglycoprotease type 2. [refseq;acc:nm_022353] 1686 OSGEPL1 220.75 217.704 1.01399
    putative tumor suppressor 101f6. [refseq;acc:nm_007022] 3051 CYB561D2 0.00001 0.00001 1
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 836 HDGFL1 231.734 222.222 1.0428
    pxr2b protein. [refseq;acc:nm_016559] 1106 PEX5L 212.945 207.109 1.02818
    pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 1708 PNPO 221.283 218.334 1.01351
    pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 1227 PYCR2 172.365 168.219 1.02465
    pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 1232 PYCR1 172.543 168.417 1.0245
    pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 2249 PC 181.091 179.999 1.00607
    pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] 1494 PDHA1 204.133 207.967 1.01878
    pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 1493 PDHA2 204.146 207.988 1.01882
    pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 1483 PDHB 198.927 202.726 1.0191
    pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] 930 PKM2 231.357 239.778 1.0364
    quaking isoform 6. [sptrembl;acc:q9p0x9] 1937 QKI 218.43 216.279 1.00995
    r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491] 3132 R3HDML 0.00001 0.00001 1
    r3h domain protein 1. [swissprot;acc:q15032] 1573 R3HDM1 218.105 214.573 1.01646
    rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] 1964 RABAC1 211.633 213.703 1.00978
    rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] 1816 RAB11FIP1 220.462 217.926 1.01164
    rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 3119 no value 0.00001 0.00001 1
    rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395] 3193 GDI2
    rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696] 3134 RABGGTA
    rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 1889 RAB3IL1 211.27 209.067 1.01054
    rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 1890 RAB3IP 211.314 209.111
    rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] 2183 RABEP1 218.062 216.624 1.00664
    rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] 2070 RACGAP1 223.199 225.008 1.0081
    rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 598 AKT1 248.463 234.095 1.06138
    rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] 600 AKT2
    rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] 599 AKT3
    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] 2195 RAD1 209.54 208.162 1.00662
    rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] 2726 RAD17 221.001 220.927 1.00033
    rad50 homolog isoform 1. [refseq;acc:nm_005732] 1312 RAD50 199.739 204.407 1.02337
    rad50-interacting protein 1. [refseq;acc:nm_021930] 11 RINT1 337 232 1.45259

    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/