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 [...,...].
    Gene Rank Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1308 to 1357 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    327 SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Measured 16067.4 19094.4 1.18839
    328 BRP44 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 1.18801
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Ranked 258.437 235.183 1.09888
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared 16442.8 20662.7 1.25664
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted 50.3803 45.4193 1.10923
    329 MTX2 metaxin 2. [swissprot;acc:o75431] Squared 41236 51807 1.25635
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked 312 284 1.09859
    PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted 50.3803 45.4193 1.10923
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured 15999.1 19007.1 1.18801
    330 CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Ranked 312 284 1.09859
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Squared 16203.4 20339.9 1.25529
    SEPT6 septin 6. [swissprot;acc:q14141] Measured 15959.9 18957.1 1.1878
    SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Rooted 50.519 45.5497 1.1091
    331 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Ranked 312 284 1.09859
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Measured 20287.2 17083.8 1.18751
    RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Squared 33100.3 41520.6 1.25439
    SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Rooted 60.6697 67.2802 1.10896
    332 NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked 312 284 1.09859
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Squared 14464.3 18142.8 1.25432
    PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Measured 5051.16 5975.51 1.183
    SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted 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 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked 312 284 1.09859
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Squared 14464.3 18142.8 1.25432
    PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Measured 5039.63 5961.83 1.18299
    334 CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared 64975.9 81151.2 1.24894
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked 312 284 1.09859
    PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 58.6096 64.9655 1.10844
    SEPT4 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] Measured 14924.4 17655.2 1.18298
    335 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared 30651.3 38253.3 1.24802
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked 312 284 1.09859
    DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Measured 3494.31 4129.6 1.18181
    RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Rooted 50.4705 45.5342 1.10841
    336 CDK2AP1 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] Ranked 312 284 1.09859
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Measured 3751.3 4431.34 1.18128
    RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 1.24789
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted 50.3167 45.4063 1.10814
    337 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Ranked 243.583 267.527 1.0983
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 20446.1 24136.4 1.18049
    CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Rooted 77.5801 70.0182 1.108
    HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Squared 46785.7 58383.2 1.24789
    338 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Ranked 243.583 267.528 1.0983
    CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Rooted 77.58 70.0181 1.108
    HIVEP1 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] Squared 46785.7 58383.2 1.24789
    HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 20446.1 24136.4 1.18049
    339 no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Ranked 243.583 267.527 1.0983
    CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Rooted 77.5797 70.0179 1.108
    HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Squared 46785.7 58383.2 1.24789
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured 20446.1 24136.4 1.18049
    340 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]

    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/