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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1780 to 1829 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    223 MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Ranked Divided 112 126 1.125
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Measured 41482.5 33356.5 1.24361
    SEPT6 septin 6. [swissprot;acc:q14141] Rooted Subtracted 113.169 123.23 10.061
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 24.52
    TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Squared Divided 40982.6 54272.3 1.32428
    224 ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured Subtracted 6417.18 7859.59 1442.41
    LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 46021.4 56813.2 10791.8
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted Divided 137.446 120.823 1.13758
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Subtracted 44.849 54.7964 9.9474
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Measured Divided 41482.5 33356.5 1.24361
    RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Ranked Subtracted 242.153 266.673 24.52
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided 185.969 165.623 1.12285
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Squared 14943.9 19771.9 1.32307
    225 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted 137.446 120.823 1.13758
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Measured 9035 7279.6 1.24114
    EPB41 protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared Subtracted 45986 56776.1 10790.1
    GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Measured 6417.19 7859.51 1442.32
    MTX1 metaxin 1. [swissprot;acc:q13505] Squared Divided 60401.6 79875.7 1.32241
    SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked Subtracted 242.153 266.673 24.52
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 226.471 201.769 1.12243
    Rooted Subtracted 55.7423 65.6839 9.9416
    226 COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Ranked Divided 239.991 269.238 1.12187
    CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured Subtracted 6417.31 7858.12 1440.81
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Rooted Divided 137.446 120.823 1.13758
    MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Measured 9035 7279.6 1.24114
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked Subtracted 242.153 266.673 24.52
    SH2D3C 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] Rooted 56.3447 66.124 9.7793
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Squared Divided 73510.2 55607.3 1.32195
    SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Subtracted 45987 56777.1 10790.1
    227 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Rooted 56.3507 66.1252 9.7745
    CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 6417.33 7857.93 1440.6
    EPB41L1 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Squared 45985.9 56776 10790.1
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Rooted Divided 137.446 120.823 1.13758
    METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Ranked Subtracted 244.126 268.604 24.478
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Measured Divided 9035 7279.6 1.24114
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Squared 73995.1 56003.7 1.32125
    THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Ranked 239.99 269.234 1.12186
    228 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 137.446 120.823 1.13758
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Subtracted 95.0526 85.3206 9.732
    ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Squared Divided 57913.5 76336.3 1.31811
    EPB41L3 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Subtracted 45986.7 56776.8 10790.1
    METAP2 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Ranked 244.126 268.604 24.478
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured Divided 9035 7279.6 1.24114
    SH2D3C 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] Ranked 226.411 202.088 1.12036
    WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Measured Subtracted 6417.81 7852.52 1434.71
    229 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked Divided 226.401 202.094 1.12028
    EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared Subtracted 45986 56776.1 10790.1
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted Divided 137.446 120.823 1.13758
    MAPK11 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] Squared 42411.6 55802.1 1.31573
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured 9035 7279.6 1.24114

    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/