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 2551 to 2600 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2551 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] FBP2 209.766 210.148 1.00182
    2552 testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] CDY1B 193.12 193.467 1.0018
    2553 chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] CDYL
    2554 testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] CDY2B
    2555 s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] MAT2A 212.953 212.572 1.00179
    2556 chromodomain y-like protein 2. [refseq;acc:nm_152342] CDYL2 193.119 193.46 1.00177
    2557 elongation factor 2 (ef-2). [swissprot;acc:p13639] EEF2 222.658 223.047 1.00175
    2558 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] GRM2
    2559 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] no value
    2560 monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] MGLL 202.395 202.042
    2561 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] FBP1 209.825 210.18 1.00169
    2562 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] GYG1 208.429 208.779 1.00168
    2563 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] ADK
    2564 protein x 0001. [refseq;acc:nm_016302] CRBN
    2565 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] GYG2
    2566 serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] AURKB 219.907 220.267 1.00164
    2567 kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] KIF23
    2568 serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9] AURKC
    2569 serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965] AURKA
    2570 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] CYLD
    2571 protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] no value 209.549 209.205
    2572 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] TAF12 203.953 204.285 1.00163
    2573 peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] PRDX4 213.347 213.005 1.00161
    2574 swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] SMARCC1 220.016 219.667 1.00159
    2575 protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] PTPN2 209.583 209.255 1.00157
    2576 beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] SNTB1 213.422 213.75 1.00154
    2577 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 192.625 192.922
    2578 beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] SNTB2 213.422 213.75
    2579 nitrilase 1. [refseq;acc:nm_005600] NIT1
    2580 utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] UTRN
    2581 dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] DTNB 213.428 213.756
    2582 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] DBT 213.422 213.75
    2583 dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] DTNA 213.415 213.743
    2584 dystrophin. [swissprot;acc:p11532] no value 213.422 213.75
    2585 angiomotin. [refseq;acc:nm_133265] AMOT
    2586 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] AMOTL2
    2587 alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] SNTA1
    2588 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] HSPD1 222.305 222.64 1.00151
    2589 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] FAM57A 212.74 212.422 1.0015
    2590 proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] PSMA6 214.605 214.287 1.00148
    2591 polybromo 1. [refseq;acc:nm_018165] PBRM1 220.02 219.696 1.00147
    2592 swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] SMARCA5
    2593 possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] SMARCA4
    2594 possible global transcription activator snf2l1. [swissprot;acc:p28370] SMARCA1
    2595 tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] BTAF1
    2596 possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] SMARCA2
    2597 ran binding protein 11. [refseq;acc:nm_016338] IPO11 212.711 212.401 1.00146
    2598 transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] TAF5 202.142 202.436 1.00145
    2599 ba207c16.2 (fragment). [sptrembl;acc:q9nql7] KIAA1432 211.662 211.361 1.00142
    2600 interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] HYAL3 224.877 225.193 1.00141

    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/