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 [...,...].
    Gene Rank Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1208 to 1257 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    302 RPL26 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked 242.326 267.008 1.10185
    303 CRKL crk-like protein. [swissprot;acc:p46109] Squared 28896.2 36767 1.27238
    PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured 22268.8 18560.4 1.1998
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
    RPL35 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
    304 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
    ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Measured 4855.46 5824.52 1.19958
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 1.11517
    305 FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 28896.2 36767 1.27238
    MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Ranked 242.339 266.986 1.1017
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured 3856.29 4624.15 1.19912
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted 203.673 182.638 1.11517
    306 no value 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 242.153 266.673 1.10126
    pnas-18. [sptrembl;acc:q9bzu3] Measured 13680.5 11409.6 1.19903
    FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 36767 1.27238
    RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted 56.3935 62.8817 1.11505
    307 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured 12365.2 14824.9 1.19892
    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] Squared 28896.4 36766.8 1.27237
    SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Rooted 50.4687 45.2733 1.11476
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 1.10126
    308 AGPAT3 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] Squared 30596.2 38919.9 1.27205
    DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Rooted 50.4687 45.2733 1.11476
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 1.19878
    RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Ranked 242.153 266.673 1.10126
    309 no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Rooted 56.185 62.6036 1.11424
    CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Squared 28900.8 36762.6 1.27203
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured 4977.8 5966.14 1.19855
    SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked 242.153 266.673 1.10126
    310 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted 95.0526 85.3206 1.11406
    CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Squared 28901.4 36762.1 1.27198
    SART1 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] Measured 4909.79 5878.79 1.19736
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked 242.153 266.673 1.10126
    311 AGPAT4 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] Squared 30566.4 38866.5 1.27154
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured 4981.52 5964.58 1.19734
    EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 242.627 267.151 1.10108
    MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted 95.0526 85.3206 1.11406
    312 no value methyltransferase like 2. [refseq;acc:nm_018396] Squared 71576.8 56326.7 1.27074
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Measured 4598.21 5500.48 1.19622
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted 95.0526 85.3206 1.11406
    RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Ranked 242.195 266.663 1.10103
    313 DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 71576.8 56326.7 1.27074
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted 95.0526 85.3206 1.11406
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured 21644.2 18098.7 1.1959
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked 232.473 211.207 1.10069
    314 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 1.27074
    METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Ranked 244.126 268.604 1.10027
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Rooted 95.0526 85.3206 1.11406
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Measured 21632.5 18090 1.19583
    315 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 1.10027

    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/