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 Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1208 to 1257 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		network_comparison
    		green
    302 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Squared 28896.2 1.27238 36767
    303 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 Ranked 242.333 1.10179 266.999
    crk-like protein. [swissprot;acc:p46109] CRKL Squared 28896.2 1.27238 36767
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Rooted 203.673 1.11517 182.638
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC Measured 22268.8 1.1998 18560.4
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value Ranked 242.339 1.1017 266.986
    cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Rooted 203.673 1.11517 182.638
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 Measured 4855.46 1.19958 5824.52
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Squared 28896.2 1.27238 36767
    305 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Rooted 203.673 1.11517 182.638
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 Ranked 242.339 1.1017 266.986
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Measured 3856.29 1.19912 4624.15
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Squared 28896.2 1.27238 36767
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value Ranked 242.153 1.10126 266.673
    pnas-18. [sptrembl;acc:q9bzu3] Measured 13680.5 1.19903 11409.6
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR Squared 28896.2 1.27238 36767
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 Rooted 56.3935 1.11505 62.8817
    307 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] GRAP2 Squared 28896.4 1.27237 36766.8
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Ranked 242.153 1.10126 266.673
    t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 Measured 12365.2 1.19892 14824.9
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] SIN3A Rooted 50.4687 1.11476 45.2733
    308 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] AGPAT3 Squared 30596.2 1.27205 38919.9
    60s ribosomal protein l34. [swissprot;acc:p49207] RPL34 Ranked 242.153 1.10126 266.673
    density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] DENR Rooted 50.4687 1.11476 45.2733
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 Measured 4977.09 1.19878 5966.44
    309 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 Squared 28900.8 1.27203 36762.6
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Ranked 242.153 1.10126 266.673
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 Measured 4977.8 1.19855 5966.14
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] no value Rooted 56.185 1.11424 62.6036
    310 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Squared 28901.4 1.27198 36762.1
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Rooted 95.0526 1.11406 85.3206
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 Ranked 242.153 1.10126 266.673
    squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] SART1 Measured 4909.79 1.19736 5878.79
    311 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] AGPAT4 Squared 30566.4 1.27154 38866.5
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 Rooted 95.0526 1.11406 85.3206
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B Ranked 242.627 1.10108 267.151
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Measured 4981.52 1.19734 5964.58
    312 60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L Ranked 242.195 1.10103 266.663
    methyltransferase like 2. [refseq;acc:nm_018396] no value Squared 71576.8 1.27074 56326.7
    myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 Rooted 95.0526 1.11406 85.3206
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] no value Measured 4598.21 1.19622 5500.48
    313 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] DYNLT1 Squared 71576.8 1.27074 56326.7
    myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] MYH2 Rooted 95.0526 1.11406 85.3206
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 Measured 21644.2 1.1959 18098.7
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Ranked 232.473 1.10069 211.207
    314 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] FZR1 Squared 71576.8 1.27074 56326.7
    methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] METAP1 Ranked 244.126 1.10027 268.604
    myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] MYH3 Rooted 95.0526 1.11406 85.3206
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 Measured 21632.5 1.19583 18090
    315 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] METAP2 Ranked 244.126 1.10027 268.604

    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/