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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2780 to 2829 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    695 SGPL1 Squared sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] 22778.5 26693.1 1.17186
    696 no value 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
    HIVEP2 Measured human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 7725.1 8647.74 1.11943
    PYCR1 Rooted pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 68.433 73.4502 1.07332
    SFRS18 Ranked sr rich protein. [refseq;acc:nm_032870] 225.293 213.64 1.05455
    697 FTH1 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 220.444 209.113 1.05419
    KCNA4 Rooted potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 63.1944 67.8162 1.07314
    OAT Squared ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] 22778.5 26693.1 1.17186
    SH3GL2 Measured sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 7105.27 7953.71 1.11941
    698 ACP1 Squared red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] 17850.2 20913.9 1.17163
    ARMET Measured armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 7101.95 7949.85 1.11939
    CSTF3 Rooted cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 128.909 120.173 1.0727
    FTMT Ranked mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 220.437 209.118 1.05413
    699 ATXN2L Rooted ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 57.0263 61.1552 1.0724
    CREG2 Ranked cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 220.438 209.118 1.05413
    HAT1 Squared histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 18148.6 21253.1 1.17106
    HDC Measured histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 7101.94 7949.84 1.11939
    700 no value 40s ribosomal protein s28. [swissprot;acc:p25112] 7161.14 8015.92 1.11936
    Ranked dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 220.438 209.118 1.05413
    Rooted ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 57.0263 61.1552 1.0724
    LSM1 Squared u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 19072.5 22327.5 1.17066
    701 ATP6V0D2 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 25852.2 30258.6 1.17045
    CSE1L Measured importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 7802.31 8731.82 1.11913
    DLGAP1 Ranked disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] 220.438 209.118 1.05413
    RAB37 Rooted ras-related protein rab-37. [swissprot;acc:q96ax2] 51.4945 48.0189 1.07238
    702 AHCYL1 Ranked putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 220.438 209.118 1.05413
    ATP6V0C Squared vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 25114 29386 1.1701
    RAB26 Rooted ras-related protein rab-26. [swissprot;acc:q9ulw5] 51.4945 48.0189 1.07238
    SH3GL3 Measured sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 7067.46 7909.27 1.11911
    703 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 6912.56 7735.12 1.11899
    KIAA0430 Ranked limkain b1. [refseq;acc:nm_019081] 220.438 209.118 1.05413
    POLR2C Rooted dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 51.4945 48.0189 1.07238
    SGCZ Squared sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] 25114 29386 1.1701
    704 no value Measured alpha-nac protein. [sptrembl;acc:q9h009] 6912.27 7734.68 1.11898
    Ranked putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 220.438 209.118 1.05413
    ACBD3 Squared golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] 25114 29386 1.1701
    STX10 Rooted syntaxin 10 (syn10). [swissprot;acc:o60499] 57.2102 53.3508 1.07234
    705 CREG1 Ranked cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 220.438 209.118 1.05413
    DIRAS1 Measured small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 6912.09 7734.41 1.11897
    SGCD Squared delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 25114 29386 1.1701
    STX6 Rooted syntaxin 6. [swissprot;acc:o43752] 57.2202 53.3639 1.07226
    706 DIRAS2 Measured di-ras2. [refseq;acc:nm_017594] 6912.08 7734.39 1.11897
    DLGAP3 Ranked disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 220.438 209.118 1.05413
    MARCH8 Squared cellular modulator of immune recognition. [refseq;acc:nm_145021] 25114 29386 1.1701
    SRP68 Rooted signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 60.6572 64.9858 1.07136
    707 ATP6V0B Squared vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] 25114 29386 1.1701
    KNG1 Ranked kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 220.438 209.118 1.05413
    RPUSD2 Measured c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 5317.78 5944.25 1.11781
    TOMM20 Rooted mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 74.8348 80.1352 1.07083
    708 no value Ranked disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 220.438 209.118 1.05413

    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/