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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2201 to 2250 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 2013 PPP1R12B 217.662 215.693 1.00913
    protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 2294 PPP1R13B 162.331 163.187 1.00527
    protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 37 PPP1R14A 322 253 1.27273
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 41 no value
    protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 39 PPP1R14D
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 592 PPP1R7 91.63 97.4011 1.06298
    protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 489 PPM1B 231.276 215.627 1.07257
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 1947 PPP1R2 125.845 127.083 1.00984
    protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 2236 no value 222.959 224.337 1.00618
    protein sck (fragment). [swissprot;acc:p98077] 2132 SHC2 221.248 222.788 1.00696
    protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 766 TRIOBP 213.804 224.226 1.04875
    protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 316 EIF1 242.694 267.017 1.10022
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 311 EIF1B 242.627 267.151 1.10108
    protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436] 3135 SEC23A 0.00001 0.00001 1
    protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437] 3127 SEC23B
    protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486] 3056 SEC24A
    protein transport protein sec24b (sec24-related protein b). [swissprot;acc:o95487] 2956 SEC24B
    protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 2910 no value
    protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855] 2903 SEC24D
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 310 SEC61A1 242.153 266.673 1.10126
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 309 SEC61A2
    protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] 360 SEC61G 243.072 266.559 1.09663
    protein x 0001. [refseq;acc:nm_016302] 2564 CRBN 208.429 208.779 1.00168
    protein x 0004. [refseq;acc:nm_016301] 10 ATPBD1C 212 309 1.45755
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 2702 PTPRB 188.435 188.311 1.00066
    protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 2571 no value 209.549 209.205 1.00164
    protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124] 2789 PTPN11 0.00001 0.00001 1
    protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] 2575 PTPN2 209.583 209.255 1.00157
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 547 CRK 207.26 194.346 1.06645
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 42 FOS 204.641 160.957 1.2714
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 553 ABL1 207.26 194.346 1.06645
    proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] 2665 FER 204.768 204.549 1.00107
    proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 2661 FES
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 555 FGR 207.26 194.346 1.06645
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 554 FYN
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 549 no value
    protocadherin 15 precursor. [swissprot;acc:q96qu1] 2463 PCDH15 235.812 235.088 1.00308
    protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] 2838 DCHS1 0.00001 0.00001 1
    protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] 1525 FAT2 219.306 223.179 1.01766
    protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 1514 COX10 213.268 209.509 1.01794
    protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [swissprot;acc:p50336] 2934 PPOX 0.00001 0.00001 1
    prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] 1941 PRPF18 198.258 196.319 1.00988
    ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 562 GULP1 220.744 207.121 1.06577
    ptd016 protein. [refseq;acc:nm_016125] 3093 no value 0.00001 0.00001 1
    purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 1838 218.984 221.446 1.01124
    puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] 2390 NPEPPS 214.966 215.799 1.00388
    putatative 28 kda protein. [refseq;acc:nm_020143] 857 PNO1 227.241 236.467 1.0406
    putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] 2011 ACOT9 193.517 191.766 1.00913
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 702 AHCYL1 220.438 209.118 1.05413
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 704 no value

    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/