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 red Interaction Map Filtered 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
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    327 septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 Measured 16067.4 19094.4 1.18839
    328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] DDX24 Ranked 258.437 235.183 1.09888
    brain protein 44. [swissprot;acc:o95563] BRP44 Measured 15999.1 19007.1 1.18801
    luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] LUC7L Squared 16442.8 20662.7 1.25664
    nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] POR Rooted 50.3803 45.4193 1.10923
    329 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] PCYT1B
    metaxin 2. [swissprot;acc:o75431] MTX2 Squared 41236 51807 1.25635
    neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 Ranked 312 284 1.09859
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Measured 15999.1 19007.1 1.18801
    330 60s ribosomal protein l32. [swissprot;acc:p02433] SNORA7A Rooted 50.519 45.5497 1.1091
    chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3 Ranked 312 284 1.09859
    huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B Squared 16203.4 20339.9 1.25529
    septin 6. [swissprot;acc:q14141] SEPT6 Measured 15959.9 18957.1 1.1878
    331 apical-like protein (apxl protein). [swissprot;acc:q13796] SHROOM2 Rooted 60.6697 67.2802 1.10896
    doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Ranked 312 284 1.09859
    pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] PCF11 Measured 20287.2 17083.8 1.18751
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Squared 33100.3 41520.6 1.25439
    332 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 Ranked 312 284 1.09859
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Squared 14464.3 18142.8 1.25432
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 Measured 5051.16 5975.51 1.183
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] SHROOM3 Rooted 60.6732 67.2827 1.10894
    333 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 Ranked 312 284 1.09859
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 Measured 5039.63 5961.83 1.18299
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 Rooted 49.0526 54.3781 1.10857
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Squared 14464.3 18142.8 1.25432
    334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 64975.9 81151.2 1.24894
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Ranked 312 284 1.09859
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 Rooted 58.6096 64.9655 1.10844
    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 Measured 14924.4 17655.2 1.18298
    335 40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 Rooted 50.4705 45.5342 1.10841
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 Ranked 312 284 1.09859
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 Measured 3494.31 4129.6 1.18181
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 Squared 30651.3 38253.3 1.24802
    336 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 Rooted 50.3167 45.4063 1.10814
    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] CDK2AP1 Ranked 312 284 1.09859
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 Measured 3751.3 4431.34 1.18128
    j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] RBPJ Squared 46785.7 58383.2 1.24789
    337 60s ribosomal protein l12. [swissprot;acc:p30050] no value Ranked 243.583 267.527 1.0983
    carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 Rooted 77.5801 70.0182 1.108
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Measured 20446.1 24136.4 1.18049
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3 Squared 46785.7 58383.2 1.24789
    338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] no value Ranked 243.583 267.528 1.0983
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Measured 20446.1 24136.4 1.18049
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 Rooted 77.58 70.0181 1.108
    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] HIVEP1 Squared 46785.7 58383.2 1.24789
    339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] no value Ranked 243.583 267.527 1.0983
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Measured 20446.1 24136.4 1.18049
    human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] HIVEP2 Squared 46785.7 58383.2 1.24789
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 Rooted 77.5797 70.0179 1.108
    340 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Measured 20446.1 24136.4 1.18049

    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/