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 886 to 935 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    Hugo
    description
    Network Comparison Type
    Interaction Map
    red
    green
    network_comparison
    222 CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted Low confidence 212.056 202.524 9.532
    MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided High confidence 112 126 1.125
    UBE2E1 ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Low confidence 203.935 214.089 1.04979
    223 GTF3C3 general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] 217.228 206.926
    MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] High confidence 112 126 1.125
    SIM1 single-minded homolog 1. [swissprot;acc:p81133] Subtracted Low confidence 212.056 202.524 9.532
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] High confidence 242.153 266.673 24.52
    224 NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Low confidence 209.649 200.129 9.52
    RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] High confidence 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
    UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Low confidence 203.933 214.059 1.04965
    225 ANKRD7 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Subtracted 216.855 207.34 9.515
    SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] High confidence 242.153 266.673 24.52
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided Low confidence 201.41 191.974 1.04915
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] High confidence 226.471 201.769 1.12243
    226 ANKRD19 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Subtracted Low confidence 216.845 207.333 9.512
    COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Divided High confidence 239.991 269.238 1.12187
    LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Low confidence 208.289 198.538 1.04911
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Subtracted High confidence 242.153 266.673 24.52
    227 ANKRD30A breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Low confidence 216.842 207.332 9.51
    METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] High confidence 244.126 268.604 24.478
    TENC1 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Divided Low confidence 216.404 206.277 1.04909
    THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] High confidence 239.99 269.234 1.12186
    228 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] Subtracted 244.126 268.604 24.478
    RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 189.45 179.944 9.506
    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] Divided High confidence 226.411 202.088 1.12036
    SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Low confidence 202.727 193.31 1.04871
    229 no value sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] Subtracted 216.546 207.063 9.483
    BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Divided High confidence 226.401 202.094 1.12028
    RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Subtracted 242.195 266.663 24.468
    TLR2 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Divided Low confidence 207.926 198.276 1.04867
    230 CCDC22 jm1 protein. [refseq;acc:nm_014008] 216.308 206.292 1.04855
    CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] High confidence 239.35 267.915 1.11934
    EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Subtracted 242.694 267.017 24.323
    LEO1 senescence downregulated leo1-like. [refseq;acc:nm_138792] Low confidence 216.546 207.063 9.483
    231 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] High confidence 226.411 202.088 24.323
    SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Divided 239.336 267.881 1.11927
    SLC9A7 solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] Subtracted Low confidence 216.546 207.063 9.483
    TIMM23 mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Divided 220.722 210.645 1.04784
    232 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Subtracted High confidence 226.401 202.094 24.307
    CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Divided 239.336 267.879 1.11926
    CYP51A1 cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Subtracted Low confidence 208.851 199.38 9.471
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Divided 214.032 204.284 1.04772
    233 no value 60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted High confidence 235.727 259.984 24.257
    CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided 239.32 267.842 1.11918
    NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Low confidence 209.649 200.129 1.04757
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted 201.41 191.974 9.436
    234 CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided High confidence 287.41 256.835 1.11905
    CYP51A1 cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 208.851 199.38 1.0475
    DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Subtracted 210.504 201.086 9.418

    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/