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 Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 873 to 922 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		description
    		red
    		green
    		network_comparison
    219 Measured transforming protein n-ras. [swissprot;acc:p01111] 16069.8 12885.6 1.24711
    Ranked myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 112 126 1.125
    Squared cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 86600.9 65229.9 1.32763
    Rooted histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 52.7146 60.0088 1.13837
    220 Measured mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 41482.5 33356.5 1.24361
    Ranked myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 112 126 1.125
    Squared cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 86600.9 65229.9 1.32763
    Rooted metastasis-associated protein mta1. [swissprot;acc:q13330] 52.7557 60.035 1.13798
    221 Measured cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 33356.5 1.24361
    Ranked myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 112 126 1.125
    Squared hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 70739 93908.8 1.32754
    Rooted spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 56.9506 64.7888 1.13763
    222 Measured cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 33356.5 1.24361
    Ranked dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 112 126 1.125
    Squared signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] 86281 65058.3 1.32621
    Rooted chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 52.7936 60.0592 1.13762
    223 Measured cytohesin 4. [swissprot;acc:q9uia0] 41482.5 33356.5 1.24361
    Ranked myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 112 126 1.125
    Squared t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 40982.6 54272.3 1.32428
    Rooted melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 137.446 120.823 1.13758
    224 Measured cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 33356.5 1.24361
    Ranked oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 185.969 165.623 1.12285
    Squared small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 14943.9 19771.9 1.32307
    Rooted hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 137.446 120.823 1.13758
    225 Measured myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 9035 7279.6 1.24114
    Ranked small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 226.471 201.769 1.12243
    Squared metaxin 1. [swissprot;acc:q13505] 60401.6 79875.7 1.32241
    Rooted melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 137.446 120.823 1.13758
    226 Measured myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 9035 7279.6 1.24114
    Ranked cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
    Squared oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 73510.2 55607.3 1.32195
    Rooted melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 137.446 120.823 1.13758
    227 Measured myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 9035 7279.6 1.24114
    Ranked thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 269.234 1.12186
    Squared oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 73995.1 56003.7 1.32125
    Rooted melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 137.446 120.823 1.13758
    228 Measured myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 9035 7279.6 1.24114
    Ranked sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 202.088 1.12036
    Squared enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 57913.5 76336.3 1.31811
    Rooted hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 137.446 120.823 1.13758
    229 Measured myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 9035 7279.6 1.24114
    Ranked breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 1.12028
    Squared mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 42411.6 55802.1 1.31573
    Rooted melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 137.446 120.823 1.13758
    230 Measured myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 9035 7279.6 1.24114
    Ranked cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 1.11934
    Squared sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 42411.6 55802.1 1.31573
    Rooted necdin. [swissprot;acc:q99608] 137.446 120.823 1.13758
    231 Measured myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 9035 7279.6 1.24114
    Ranked likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 267.881 1.11927

    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
    - 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/