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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 812 to 861 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    812 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] NAPA 212.386 221.785 1.04425
    813 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] C20orf3
    814 synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] SNAP29
    815 syntaxin 1b. [swissprot;acc:q15531] STX1B
    816 melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] MRPL28
    817 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] RFXANK
    818 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] RGL1 168.592 161.452 1.04422
    819 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] POLR2I 228.563 238.668 1.04421
    820 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] MRPS2 221.716 231.501 1.04413
    821 u3 snornp protein 4 homolog. [refseq;acc:nm_033416] IMP4 221.676 231.453 1.0441
    822 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] EIF3B 243.067 232.805 1.04408
    823 transcription factor iib. [refseq;acc:nm_013242] C16orf80 206.068 197.471 1.04354
    824 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] SFRS8
    825 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] WIPF1 206.214 197.614 1.04352
    826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] HTATIP 223.186 213.912 1.04335
    827 loh1cr12. [refseq;acc:nm_058169] LOH12CR1 230.087 220.579 1.0431
    828 unr protein. [swissprot;acc:o75534] CSDE1
    829 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] SEPT4 135.844 130.259 1.04288
    830 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] PARK2 231.734 222.222 1.0428
    831 hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] no value
    832 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
    833 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] PSIP1
    834 60s ribosomal protein l8. [swissprot;acc:p25120] RPL8
    835 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] HDGF
    836 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] HDGFL1
    837 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] DDX6
    838 rw1 protein (fragment). [swissprot;acc:q92545] TMEM131
    839 stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] CLEC11A 177.776 170.499 1.04268
    840 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] TOMM20 198.781 190.66 1.04259
    841 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] PEX19
    842 jm1 protein. [refseq;acc:nm_014008] CCDC22 219.762 210.806 1.04248
    843 trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] GART 218.521 227.796 1.04244
    844 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] CLEC3A 178.033 170.82 1.04223
    845 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] LSM1 228.599 219.399 1.04193
    846 methyltransferase like 2. [refseq;acc:nm_018396] no value 147.211 153.371 1.04184
    847 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] DYNLT1
    848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] FZR1
    849 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] PCSK5
    850 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] CPSF4 107.842 112.329 1.04161
    851 trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012
    852 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] HPRT1 193.114 185.412 1.04154
    853 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 108.289 112.772 1.0414
    854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1
    855 tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] CLEC3B 178.514 171.42 1.04138
    856 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] XPR1 215.028 206.623 1.04068
    857 putatative 28 kda protein. [refseq;acc:nm_020143] PNO1 227.241 236.467 1.0406
    858 syntaxin 12. [refseq;acc:nm_177424] STX12 217.446 208.997 1.04043
    859 60s ribosomal protein l39. [swissprot;acc:p02404] no value 234.025 224.958 1.04031
    860 60s ribosomal protein l18a. [swissprot;acc:q02543]
    861 40s ribosomal protein s19. [swissprot;acc:p39019] RPS19

    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/