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 6358 to 6407 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    1590 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] PUF60 Measured 6364.01 6819.38 1.07155
    puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] NPEPPS Rooted 62.7026 64.9366 1.03563
    thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] TYMS Ranked 225.119 228.769 1.01621
    1591 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] no value
    leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] LTA4H Rooted 62.7026 64.9366 1.03563
    multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] no value Measured 6364.01 6819.38 1.07155
    receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] ERBB2 Squared 29261.2 32474.1 1.1098
    1592 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] PSMD11 Measured 5853.1 6271.79 1.07153
    dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] DHODH Rooted 62.7026 64.9366 1.03563
    receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] ERBB4 Squared 29261.2 32473.8 1.10979
    stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] SDF2 Ranked 225.119 228.769 1.01621
    1593 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] HACL1 Squared 29261.2 32473.8 1.10979
    proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] PCNA Measured 4977.77 5333.78 1.07152
    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] ACP1 Rooted 60.0929 62.2327 1.03561
    stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] SDF2L1 Ranked 225.119 228.769 1.01621
    1594 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] JPH4 222.133 225.731 1.0162
    receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] ERBB3 Squared 29261.2 32473.8 1.10979
    transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] VCP Rooted 64.5338 66.8288 1.03556
    transportin-sr; importin 12. [refseq;acc:nm_012470] TNPO3 Measured 5184.94 5555.76 1.07152
    1595 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] no value Ranked 222.134 225.731 1.01619
    dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] MCM3 Rooted 55.3706 57.3394 1.03556
    proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] no value Measured 6351.32 6805.39 1.07149
    tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] YARS Squared 17195.6 19080.9 1.10964
    1596 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] AP1G1 Ranked 222.134 225.731 1.01619
    enigma protein; lim domain protein. [refseq;acc:nm_005451] no value Measured 5665.34 6070.32 1.07148
    kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] KEAP1 Rooted 55.3706 57.3394 1.03556
    p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] ING4 Squared 25787.8 28614.7 1.10962
    1597 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] AP1S3 Ranked 222.134 225.731 1.01619
    eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] EIF3D Measured 5665.34 6070.32 1.07148
    lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] LIN7B Squared 29261.6 32468.9 1.10961
    mesoderm induction early response 1. [refseq;acc:nm_020948] no value Rooted 64.6178 66.9075 1.03543
    1598 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] AP1S1 Ranked 222.134 225.731 1.01619
    lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] no value Measured 5068.17 5430.41 1.07147
    myosin viia. [swissprot;acc:q13402] MYO7A Squared 26326.2 29206.2 1.1094
    proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] PSMA3 Rooted 64.6178 66.9075 1.03543
    1599 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] RPS24 Measured 5184.45 5554.97 1.07147
    dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] DTNBP1 Ranked 217.871 214.404 1.01617
    fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] FBP1 Rooted 64.7608 67.05 1.03535
    ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] UBE2B Squared 26326.2 29206.2 1.1094
    1600 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] HRSP12 Measured 6336.22 6788.96 1.07145
    adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] AP2B1 Ranked 222.103 225.675 1.01608
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] FBP2 Rooted 64.7842 67.0713 1.0353
    ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] UBE2A Squared 26326.2 29206.2 1.1094
    1601 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] RAPSN 29238.6 32434.1 1.10929
    phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] PMM2 Ranked 217.268 213.842 1.01602
    spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] SPTBN2 Measured 5232.14 5605.8 1.07142
    tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] no value Rooted 68.186 70.5859 1.0352
    1602 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] CSNK2A1P Squared 17081.4 18947.6 1.10925
    dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] TOP3A Rooted 61.8653 64.0396 1.03515
    phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] PMM1 Ranked 217.334 213.914 1.01599

    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/