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 Value Type description Hugo Network Comparison 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
    		Value Type
    		description
    		Hugo
    		red
    		green
    		network_comparison
    327 Rooted bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] PAPSS1 50.3803 45.4193 1.10923
    328 Measured brain protein 44. [swissprot;acc:o95563] BRP44 15999.1 19007.1 1.18801
    Ranked atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] DDX24 258.437 235.183 1.09888
    Squared luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] LUC7L 16442.8 20662.7 1.25664
    Rooted nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] POR 50.3803 45.4193 1.10923
    329 Measured septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 15999.1 19007.1 1.18801
    Ranked neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 312 284 1.09859
    Squared metaxin 2. [swissprot;acc:o75431] MTX2 41236 51807 1.25635
    Rooted 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 50.3803 45.4193 1.10923
    330 Measured septin 6. [swissprot;acc:q14141] SEPT6 15959.9 18957.1 1.1878
    Ranked chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3 312 284 1.09859
    Squared huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B 16203.4 20339.9 1.25529
    Rooted 60s ribosomal protein l32. [swissprot;acc:p02433] SNORA7A 50.519 45.5497 1.1091
    331 Measured pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] PCF11 20287.2 17083.8 1.18751
    Ranked doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 312 284 1.09859
    Squared ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 33100.3 41520.6 1.25439
    Rooted apical-like protein (apxl protein). [swissprot;acc:q13796] SHROOM2 60.6697 67.2802 1.10896
    332 Measured pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 5051.16 5975.51 1.183
    Ranked neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 312 284 1.09859
    Squared nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 14464.3 18142.8 1.25432
    Rooted shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] SHROOM3 60.6732 67.2827 1.10894
    333 Measured nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 5039.63 5961.83 1.18299
    Ranked neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 312 284 1.09859
    Squared nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 14464.3 18142.8 1.25432
    Rooted nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 49.0526 54.3781 1.10857
    334 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] SEPT4 14924.4 17655.2 1.18298
    Ranked neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 312 284 1.09859
    Squared ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 64975.9 81151.2 1.24894
    Rooted pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 58.6096 64.9655 1.10844
    335 Measured probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 3494.31 4129.6 1.18181
    Ranked chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 312 284 1.09859
    Squared ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 30651.3 38253.3 1.24802
    Rooted 40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 50.4705 45.5342 1.10841
    336 Measured dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 3751.3 4431.34 1.18128
    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] CDK2AP1 312 284 1.09859
    Squared j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] RBPJ 46785.7 58383.2 1.24789
    Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 50.3167 45.4063 1.10814
    337 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value 20446.1 24136.4 1.18049
    Ranked 60s ribosomal protein l12. [swissprot;acc:p30050] 243.583 267.527 1.0983
    Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3 46785.7 58383.2 1.24789
    Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 77.5801 70.0182 1.108
    338 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 20446.1 24136.4 1.18049
    Ranked 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] no value 243.583 267.528 1.0983
    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] HIVEP1 46785.7 58383.2 1.24789
    Rooted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 77.58 70.0181 1.108
    339 Measured homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 20446.1 24136.4 1.18049
    Ranked dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] no value 243.583 267.527 1.0983
    Squared human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] HIVEP2 46785.7 58383.2 1.24789
    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] CPB2 77.5797 70.0179 1.108
    340 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value 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/