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 Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1308 to 1357 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 611 HIST3H3 247.47 233.441 1.0601
    histone h4. [swissprot;acc:p02304] 946 no value 227.765 219.902 1.03576
    histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] 1342 SUV39H1 226.433 231.491 1.02234
    histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] 1340 SUV39H2
    hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 645 HTATSF1 217.67 230.596 1.05938
    hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 1503 KRR1 242.181 237.834 1.01828
    hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] 643 HRBL 217.67 230.596 1.05938
    hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] 1613 HTATIP2 182.378 185.241 1.0157
    hmg2 like. [refseq;acc:nm_145205] 2799 HMGB4 0.00001 0.00001 1
    homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] 2194 PROX1 209.54 208.162 1.00662
    homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 582 BARX1 237.28 252.492 1.06411
    homeobox protein barh-like 2. [swissprot;acc:q9umq3] 587 BARX2
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 557 CUTL2 207.272 194.371 1.06637
    homeobox protein dlx-2. [swissprot;acc:q07687] 2337 DLX2 229.258 230.294 1.00452
    homeobox protein dlx-3. [swissprot;acc:o60479] 2340 DLX3
    homeobox protein dlx-5. [swissprot;acc:p56178] 2338 DLX5
    homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 1167 EN2 219.399 213.784 1.02626
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 7 HLX 215 322 1.49767
    homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 614 HOXA10 214.257 202.125 1.06002
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 686 no value 132.413 125.389 1.05602
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 685 HOXA5
    homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 616 HOXA9 214.257 202.132 1.05999
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 680 HOXB4 132.413 125.389 1.05602
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 684 HOXB5
    homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 615 HOXB9 214.257 202.132 1.05999
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 679 no value 132.413 125.389 1.05602
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 681 HOXC5
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 682 no value
    homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 617 HOXC9 214.257 202.135 1.05997
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 683 HOXD4 132.413 125.389 1.05602
    homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 632 HOXD9 214.254 202.166 1.05979
    homeobox protein meis1. [swissprot;acc:o00470] 1783 MEIS1 206.332 203.874 1.01206
    homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] 1784 MEIS2
    homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] 1788 MEIS3
    homeobox protein nkx-6.1. [swissprot;acc:p78426] 2859 NKX6-1 0.00001 0.00001 1
    homeobox protein otx1. [swissprot;acc:p32242] 1520 OTX1 244.367 240.098 1.01778
    homeobox protein otx2. [swissprot;acc:p32243] 1521 OTX2 244.478 240.212 1.01776
    homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 1709 HHEX 198.014 195.385 1.01346
    homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] 1128 SIX1 221.286 215.399 1.02733
    homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] 1129 SIX2 221.285 215.401 1.02732
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 107 HOMER1 252.309 201.998 1.24907
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 104 HOMER2 252.371 202.016 1.24926
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 108 HOMER3 252.296 201.995 1.24902
    homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011] 3196 HERPUD1 0.00001 0.00001 1
    homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 3053 HGD
    homolog of yeast maf1. [refseq;acc:nm_032272] 1977 MAF1 209.539 207.529 1.00969
    hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469] 3172 LIPE 0.00001 0.00001 1
    hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 289 no value 272.781 246.892 1.10486
    hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] 2231 SYVN1 221.842 223.246 1.00633
    hsgcn1 (fragment). [sptrembl;acc:q99736] 2712 GCN1L1 220.521 220.395 1.00057

    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/