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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 50974 to 51023 of 66312 in total
    Network Comparison Type  : Subtracted
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    2228 Measured sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] SALL3 High confidence 265.18 5783.72 6048.9
    Ranked hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] CDC37 1.303 223.888 225.191
    ran guanine nucleotide release factor; homolog of yeast mog1; likely ortholog of mouse ran guanine nucleotide release factor. [refseq;acc:nm_014185] RANGRF Low confidence 3.717 201.12 197.403
    Squared myosin heavy chain, nonmuscle type b (cellular myosin heavy chain, type b) (nonmuscle myosin heavy chain-b) (nmmhc-b). [swissprot;acc:p35580] MYH10 1705.5 45532.1 43826.6
    protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] MEMO1P High confidence 1709.5 15537.9 17247.4
    Rooted adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] ARFGAP3 1.3908 60.8609 62.2517
    gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] GABRA6 Low confidence 2.4828 71.6375 74.1203
    2229 Measured arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] RERE High confidence 265.18 5783.76 6048.94
    peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin f). [swissprot;acc:p30405] PPIF Low confidence 248.91 8059.49 8308.4
    Ranked 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] no value High confidence 1.284 199.129 200.413
    ring finger protein 2. [refseq;acc:nm_007212] RNF2 Low confidence 3.716 202.479 198.763
    Squared karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] TNPO2 High confidence 1706.9 25712.1 27419
    peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] PRDX5 Low confidence 1705.4 45260.9 43555.5
    Rooted serine/threonine protein kinase mask; ste20-like kinase mst4. [refseq;acc:nm_016542] no value 2.4828 72.7441 75.2269
    solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] SLC23A2 High confidence 1.3908 60.8609 62.2517
    2230 Measured hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] HIF3A Low confidence 248.88 7974.48 8223.36
    ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] USP8 High confidence 265.18 5783.73 6048.91
    Ranked ral-a exchange factor ralgps2. [refseq;acc:nm_152663] RALGPS2 Low confidence 3.716 195.813 192.097
    sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] SAP30 High confidence 1.284 199.129 200.413
    Squared calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] CAPNS1 Low confidence 1705.3 45633.7 43928.4
    zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] ZNRD1 High confidence 1701.7 16044.8 17746.5
    Rooted dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733] MAP2K7 1.3908 60.8609 62.2517
    gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] GABRG2 Low confidence 2.4828 71.6377 74.1205
    2231 Measured f-box and leucine-rich repeat protein 2; f-box protein containing leucine-rich repeats. [refseq;acc:nm_012157] FBXL2 248.81 8054.19 8303
    rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] ROD1 High confidence 265.18 5783.73 6048.91
    Ranked clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] AP2M1 1.284 199.129 200.413
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Low confidence 3.716 151.012 154.728
    Squared grancalcin. [swissprot;acc:p28676] GCA 1705.2 45633.6 43928.4
    hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] KRR1 High confidence 1699.3 15639.2 17338.5
    Rooted gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] GABRA4 Low confidence 2.4828 71.6375 74.1203
    ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] KHK High confidence 1.3903 60.8787 62.269
    2232 Measured f-box protein fbl2. [refseq;acc:nm_032875] FBXL20 Low confidence 248.78 8054.31 8303.09
    polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] PTBP2 High confidence 265.18 5783.73 6048.91
    Ranked atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] ABCC10 1.284 199.129 200.413
    myosin regulatory light chain mrcl2. [refseq;acc:nm_033546] no value Low confidence 3.715 200.314 196.599
    Squared polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] GALNT2 High confidence 1697.9 28320.2 30018.1
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI Low confidence 1705.2 45633.6 43928.4
    Rooted ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] FTSJ3 2.4828 73.2463 75.7291
    purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] no value High confidence 1.3903 60.8787 62.269
    2233 Measured adaptor-associated kinase 1. [refseq;acc:nm_014911] AAK1 265.18 5783.73 6048.91
    eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] EIF3K Low confidence 248.75 7781.68 8030.43
    Ranked lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754] MAN2B1 High confidence 1.284 199.129 200.413
    myosin regulatory light chain 2, nonsarcomeric (myosin rlc). [swissprot;acc:p19105] no value Low confidence 3.715 200.314 196.599
    Squared hmg2 like. [refseq;acc:nm_145205] HMGB4 1705.1 45538.4 43833.3
    similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] GALNTL1 High confidence 1697.9 28320.2 30018.1
    Rooted gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] GABRE Low confidence 2.4828 71.6375 74.1203
    peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] PPIH High confidence 1.3873 75.1279 76.5152
    2234 Measured atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] ATN1 265.18 5783.7 6048.88
    ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] no value Low confidence 248.75 7781.68 8030.43
    Ranked myosin regulatory light chain 2, smooth muscle isoform (myosin rlc) (lc20). [swissprot;acc:p24844] MYL9 3.715 200.307 196.592

    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/