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 Gene description Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 61224 to 61273 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    4425 zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098] ZNF8 Subtracted Ranked 197.793 195.963 1.83
    4426 early growth response protein 3 (egr-3) (zinc finger protein pilot). [swissprot;acc:q06889] EGR3 Divided Squared 46053.5 45044.6 1.0224
    inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] IMPDH1 Subtracted 46866 45896.2 969.8
    kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] KIF3B Measured 8590.09 8434.52 155.57
    krueppel-like factor 7 (ubiquitous krueppel-like factor). [swissprot;acc:o75840] KLF7 Divided 9143.92 9323.55 1.01964
    lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] LMX1A Rooted 69.9633 71.6393 1.02396
    nadh-ubiquinone oxidoreductase 42 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-42kd) (ci-42kd). [swissprot;acc:o95299] NDUFA10 Subtracted 70.7716 72.5055 1.7339
    zinc finger protein 324 (zinc finger protein zf5128). [swissprot;acc:o75467] ZNF324 Ranked 197.793 195.963 1.83
    zinc finger protein 398 (zinc finger dna binding protein p52/p71). [swissprot;acc:q8td17] ZNF282 Divided 195.964 1.00933
    4427 early growth response protein 4 (egr-4) (at133). [swissprot;acc:q05215] EGR4 Squared 46051.3 45042.3 1.0224
    heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] HNRNPA2B1 Subtracted Measured 7634.71 7790.06 155.35
    lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] LMX1B Divided Rooted 69.9633 71.6393 1.02396
    p120e4f. [refseq;acc:nm_004424] E4F1 Ranked 197.793 195.964 1.00933
    similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] EVI5L Subtracted Squared 46482.1 45515.1 967
    transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] MORF4L1 Divided Measured 7780.54 7933.09 1.01961
    tumor antigen slp-8p. [refseq;acc:nm_016516] VPS54 Subtracted Rooted 71.3012 73.0349 1.7337
    zinc finger protein 93 (zinc finger protein htf34) (fragment). [swissprot;acc:p35789] ZNF93 Ranked 197.793 195.963 1.83
    4428 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] BRD2 Divided Rooted 75.2147 77.0117 1.02389
    coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] ARCN1 Subtracted Squared 45161 44195.7 965.3
    cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] COPS4 Rooted 71.3012 73.0349 1.7337
    early growth response protein 2 (egr-2) (krox-20 protein) (at591). [swissprot;acc:p11161] EGR2 Divided Squared 46053.4 45044.6 1.0224
    protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822] C21orf2 Subtracted Measured 7730.36 7885.54 155.18
    synapsin iii. [swissprot;acc:o14994] SYN3 Divided 8229.39 8390.59 1.01959
    zinc finger protein 33a (zinc finger protein kox31) (ha0946). [swissprot;acc:q06730] ZNF37A Subtracted Ranked 197.793 195.963 1.83
    zinc finger protein 407. [refseq;acc:nm_017757] ZNF407 Divided 195.964 1.00933
    4429 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] AIP Subtracted Measured 8303.78 8458.91 155.13
    complement component c7 precursor. [swissprot;acc:p10643] C7 Divided Rooted 70.0487 71.7192 1.02385
    early growth response protein 1 (egr-1) (krox-24 protein) (zif268) (nerve growth factor-induced protein a) (ngfi-a) (transcription factor etr103) (zinc finger protein 225) (at225). [swissprot;acc:p18146] EGR1 Squared 46064.7 45056.3 1.02238
    histone-lysine n-methyltransferase, h3 lysine-79 specific (ec 2.1.1.43) (histone h3-k79 methyltransferase) (h3-k79-hmtase) (dot1-like protein). [swissprot;acc:q8tek3] DOT1L Subtracted Rooted 71.3012 73.0349 1.7337
    inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] IMPDH2 Squared 46870.4 45905.2 965.2
    similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_033196] no value Ranked 197.793 195.963 1.83
    synapsin ii. [swissprot;acc:q92777] SYN2 Divided Measured 8229.39 8390.59 1.01959
    zinc finger protein 38 homolog (zfp-38) (ny-ren-21 antigen). [swissprot;acc:q9y5a6] ZSCAN21 Ranked 197.793 195.964 1.00933
    4430 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] CRAT Subtracted Measured 8170.81 8325.77 154.96
    myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] no value Rooted 71.0754 72.8088 1.7334
    sec13-related protein. [swissprot;acc:p55735] SEC13 Divided 76.2014 78.0165 1.02382
    solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] SLC27A3 Subtracted Squared 46028 45065 963
    synapsin i (brain protein 4.1). [swissprot;acc:p17600] SYN1 Divided Measured 8229.39 8390.59 1.01959
    wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] WASF3 Squared 47038.1 46011.1 1.02232
    zinc finger protein 143 (sph-binding factor). [swissprot;acc:p52747] ZNF143 Ranked 197.793 195.964 1.00933
    zinc finger protein 275. [swissprot;acc:q9nsd4] ZNF275 Subtracted 195.963 1.83
    4431 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Divided Squared 40260.5 39382.4 1.0223
    associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Subtracted Rooted 71.0627 69.3294 1.7333
    heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] HNRPA3 Measured 7633.6 7788.52 154.92
    proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] PSMB4 Divided Rooted 72.0029 73.7135 1.02376
    solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] SLC27A5 Subtracted Squared 46028 45065.1 962.9
    transcription factor sp1. [swissprot;acc:p08047] no value Divided Measured 9146.05 9324.86 1.01955
    zinc finger protein 228. [swissprot;acc:q9uju3] ZNF228 Subtracted Ranked 197.793 195.963 1.83
    zinc finger protein 319. [swissprot;acc:q9p2f9] ZNF319 Divided 195.964 1.00933
    4432 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] AIPL1 Subtracted Measured 8302.46 8457.37 154.91

    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/