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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1325 to 1374 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    332 NEUROD6 Ranked neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 312 284 1.09859
    NUBP1 Squared nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 14464.3 18142.8 1.25432
    PLRG1 Measured pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 5051.16 5975.51 1.183
    SHROOM3 Rooted shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 60.6732 67.2827 1.10894
    333 GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 49.0526 54.3781 1.10857
    NEUROD1 Ranked neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 312 284 1.09859
    NUBP2 Squared nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 14464.3 18142.8 1.25432
    PRPF19 Measured nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299
    334 CANT1 Squared ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 81151.2 1.24894
    NEUROD4 Ranked neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 312 284 1.09859
    PLRG1 Rooted pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 58.6096 64.9655 1.10844
    SEPT4 Measured 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] 14924.4 17655.2 1.18298
    335 C15orf15 Squared ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 30651.3 38253.3 1.24802
    CHD5 Ranked chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 312 284 1.09859
    DDX56 Measured probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
    RPS11 Rooted 40s ribosomal protein s11. [swissprot;acc:p04643] 50.4705 45.5342 1.10841
    336 CDK2AP1 Ranked cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 312 284 1.09859
    POLE4 Measured dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 3751.3 4431.34 1.18128
    RBPJ Squared j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 46785.7 58383.2 1.24789
    RPL11 Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] 50.3167 45.4063 1.10814
    337 no value Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 1.18049
    Ranked 60s ribosomal protein l12. [swissprot;acc:p30050] 243.583 267.527 1.0983
    CPA6 Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] 77.5801 70.0182 1.108
    HIVEP3 Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 46785.7 58383.2 1.24789
    338 no value Ranked 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 267.528 1.0983
    CPA3 Rooted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 77.58 70.0181 1.108
    HIVEP1 Squared zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] 46785.7 58383.2 1.24789
    HOXB4 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 1.18049
    339 no value Ranked dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 243.583 267.527 1.0983
    CPB2 Rooted plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 77.5797 70.0179 1.108
    HIVEP2 Squared human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 46785.7 58383.2 1.24789
    HOXC5 Measured homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 20446.1 24136.4 1.18049
    340 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
    MYEF2 Ranked myelin gene expression factor 2. [refseq;acc:nm_016132] 235.383 258.476 1.09811
    PRPF19 Rooted nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 58.4926 64.8047 1.10791
    RRM2B Squared ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 32117 40054 1.24713
    341 no value Ranked 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
    HOXD4 Measured homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 20446.1 24136.4 1.18049
    RRM1 Squared ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 32056.4 39965.8 1.24673
    SSB Rooted lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 51.9812 57.5858 1.10782
    342 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 49.2715 54.5757 1.10765
    HGS Squared hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 70830.5 56822 1.24653
    HOXB5 Measured homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 20446.1 24136.4 1.18049
    RPS20 Ranked 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 267.21 1.09737
    343 no value Rooted 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 50.3169 45.4333 1.10749
    COG7 Squared conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] 70830.5 56822 1.24653
    HOXA5 Measured homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 20446.1 24136.4 1.18049
    PRMT3 Ranked protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 265.136 1.0973
    344 no value Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 20446.1 24136.4 1.18049
    Ranked 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 241.625 265.136 1.0973

    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/