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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 262 to 311 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 1249 no value 219.354 224.7 1.02437
    alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] 812 NAPA 212.386 221.785 1.04425
    alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] 1961 ABHD1 211.633 213.703 1.00978
    alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] 1959 ABHD3
    alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083] 2829 ASPSCR1 0.00001 0.00001 1
    amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 637 PPAT 228.639 242.258 1.05957
    aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] 1420 ACY1 203.979 208.229 1.02084
    aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 2064 AASS 207.655 205.939 1.00833
    aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 2544 AMT 212.67 212.262 1.00192
    ammecr1 protein. [refseq;acc:nm_015365] 1577 AMMECR1 222.585 218.982 1.01645
    amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 52 AMPD2 133 105 1.26667
    amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 139 APBA1 271.752 225.68 1.20415
    amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] 2490 APPBP1 194.527 195.08 1.00284
    amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380] 3191 APPBP2 0.00001 0.00001 1
    anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 2636 ANAPC11 195.635 195.384 1.00128
    anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] 2663 ANAPC10 204.768 204.549 1.00107
    anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 2679 ANAPC2 190.142 189.959 1.00096
    androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 240 AIG1 227.357 254.15 1.11785
    angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] 2586 AMOTL2 213.422 213.75 1.00154
    angiomotin. [refseq;acc:nm_133265] 2585 AMOT
    anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 143 ANLN 59 49 1.20408
    ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] 2519 ANK2 215.835 216.341 1.00234
    ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] 2518 ANK3
    ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] 805 ANKRA2 212.386 221.785 1.04425
    annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 1088 ANXA11 219.673 213.378 1.0295
    annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 1094 ANXA7 219.655 213.385 1.02938
    antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] 2418 SERPINC1 218.2 218.984 1.00359
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] 169 ATG3 82.5916 98.0548 1.18722
    apical-like protein (apxl protein). [swissprot;acc:q13796] 362 SHROOM2 231.492 211.136 1.09641
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 248 no value 237.302 212.41 1.11719
    apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 1606 APOA1BP 207.916 204.662 1.0159
    apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] 2151 APOB 217.871 219.366 1.00686
    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 233.942 228.46 1.024
    apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 1014 AATF 243.045 235.422 1.03238
    apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 1132 API5 218.484 212.675 1.02731
    apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 1111 no value 217.99 212.123 1.02766
    apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 2421 AIFM2 210.205 209.454 1.00359
    apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 2531 APEX2 216.264 215.787 1.00221
    aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 2690 AQP4 188.191 188.046 1.00077
    aquaporin 5. [swissprot;acc:p55064] 2692 AQP5 188.192 188.048
    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] 2691 AQP2 188.193
    aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 2694 AQP1 188.223 188.081 1.00075
    arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 1184 GIT1 216.729 222.334 1.02586
    arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 1110 GIT2 216.78 222.782 1.02769
    arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 947 SORBS2 212.51 205.191 1.03567
    arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 1885 ARG1 204.44 206.615 1.01064
    arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 1886 ARG2 204.512 206.682 1.01061
    arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 1379 RERE 218.47 213.875 1.02148
    arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 1478 SFRS10 215.122 211.066 1.01922
    argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 2108 ASL 216.36 217.93 1.00726

    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/