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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 694 to 743 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    anion exchange protein 2 (non-erythroid band 3-like protein) (bnd3l). [swissprot;acc:p04920] 3888 SLC4A2 Low confidence 204.559 201.988 1.01273
    ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] 2519 ANK2 High confidence 215.835 216.341 1.00234
    4158 Low confidence 202.624 200.519 1.0105
    ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] 2518 ANK3 High confidence 215.835 216.341 1.00234
    4157 Low confidence 202.624 200.519 1.0105
    ankyrin repeat and btb (poz) domain containing 1 isoform 1; elongation factor 1a binding protein. [refseq;acc:nm_032548] 595 ABTB1 205.485 199.453 1.03024
    ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 260 ANKRD7 216.855 207.34 1.04589
    ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] 805 ANKRA2 High confidence 212.386 221.785 1.04425
    4203 Low confidence 203.592 201.541 1.01018
    annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 1088 ANXA11 High confidence 219.673 213.378 1.0295
    1400 Low confidence 203.717 199.354 1.02189
    annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 1094 ANXA7 High confidence 219.655 213.385 1.02938
    1394 Low confidence 203.731 199.363 1.02191
    antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] 2418 SERPINC1 High confidence 218.2 218.984 1.00359
    2731 Low confidence 199.881 196.448 1.01748
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] 169 ATG3 High confidence 82.5916 98.0548 1.18722
    4769 Low confidence 177.446 176.597 1.00481
    apical-like protein (apxl protein). [swissprot;acc:q13796] 362 SHROOM2 High confidence 231.492 211.136 1.09641
    1029 Low confidence 204.847 199.989 1.02429
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 248 no value High confidence 237.302 212.41 1.11719
    484 Low confidence 203.821 197.291 1.0331
    apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 1606 APOA1BP High confidence 207.916 204.662 1.0159
    2607 Low confidence 199.85 196.339 1.01788
    apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] 2151 APOB High confidence 217.871 219.366 1.00686
    3097 Low confidence 202.108 198.827 1.0165
    apolipoprotein e receptor 2 isoform 1 precursor; apolipoprotein e receptor 2. [refseq;acc:nm_004631] 4825 LRP8 203.899 203.124 1.00382
    apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] 1293 CASP3 High confidence 233.942 228.46 1.024
    3279 Low confidence 200.06 196.969 1.01569
    apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 1014 AATF High confidence 243.045 235.422 1.03238
    3623 Low confidence 201.429 198.604 1.01422
    apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 844 API5 194.659 189.74 1.02592
    1132 High confidence 218.484 212.675 1.02731
    apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 1111 no value 217.99 212.123 1.02766
    1416 Low confidence 199.817 195.566 1.02174
    apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 1462 AIFM2 200.475 196.24 1.02158
    2421 High confidence 210.205 209.454 1.00359
    aprataxin isoform a; ataxia 1, early onset with hypoalbuminemia. [refseq;acc:nm_175073] 3127 APTX Low confidence 200.082 196.855 1.01639
    apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 710 APEX2 202.569 197.109 1.0277
    2531 High confidence 216.264 215.787 1.00221
    aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 1768 AQP4 Low confidence 195.404 191.524 1.02026
    2690 High confidence 188.191 188.046 1.00077
    aquaporin 5. [swissprot;acc:p55064] 1792 AQP5 Low confidence 195.447 191.588 1.02014
    2692 High confidence 188.192 188.048 1.00077
    aquaporin 6 (aquaporin-2 like) (hkid). [swissprot;acc:q13520] 1656 AQP6 Low confidence 195.243 191.284 1.0207
    aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 1790 AQP2 195.447 191.588 1.02014
    2691 High confidence 188.193 188.048 1.00077
    aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 1804 AQP1 Low confidence 195.454 191.599 1.02012
    2694 High confidence 188.223 188.081 1.00075
    arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 1006 GIT1 Low confidence 206.183 201.259 1.02447
    1184 High confidence 216.729 222.334 1.02586

    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/