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 1213 to 1262 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    304 no value Ranked 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
    ABL1 Squared proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 28896.2 36767 1.27238
    PRPF31 Measured pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 4855.46 5824.52 1.19958
    PSCD4 Rooted cytohesin 4. [swissprot;acc:q9uia0] 203.673 182.638 1.11517
    305 FYN Squared proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 28896.2 36767 1.27238
    MRPL2 Ranked mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] 242.339 266.986 1.1017
    OSR1 Measured odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
    PSCD3 Rooted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 203.673 182.638 1.11517
    306 no value Measured pnas-18. [sptrembl;acc:q9bzu3] 13680.5 11409.6 1.19903
    Ranked 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 1.10126
    FGR Squared proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 28896.2 36767 1.27238
    RBM39 Rooted rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 56.3935 62.8817 1.11505
    307 CCT3 Measured t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 12365.2 14824.9 1.19892
    GRAP2 Squared 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] 28896.4 36766.8 1.27237
    SIN3A Rooted transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 50.4687 45.2733 1.11476
    SRR Ranked serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 242.153 266.673 1.10126
    308 AGPAT3 Squared 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] 30596.2 38919.9 1.27205
    DENR Rooted density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 50.4687 45.2733 1.11476
    DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 4977.09 5966.44 1.19878
    RPL34 Ranked 60s ribosomal protein l34. [swissprot;acc:p49207] 242.153 266.673 1.10126
    309 no value Rooted u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 56.185 62.6036 1.11424
    CUTL1 Squared ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 28900.8 36762.6 1.27203
    DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 4977.8 5966.14 1.19855
    SEC61A2 Ranked protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 242.153 266.673 1.10126
    310 no value Rooted myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 95.0526 85.3206 1.11406
    CUTL2 Squared homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 28901.4 36762.1 1.27198
    SART1 Measured 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] 4909.79 5878.79 1.19736
    SEC61A1 Ranked protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 266.673 1.10126
    311 AGPAT4 Squared 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] 30566.4 38866.5 1.27154
    DVL3 Measured segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 4981.52 5964.58 1.19734
    EIF1B Ranked protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 242.627 267.151 1.10108
    MYH4 Rooted myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 95.0526 85.3206 1.11406
    312 no value Measured u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 4598.21 5500.48 1.19622
    Squared methyltransferase like 2. [refseq;acc:nm_018396] 71576.8 56326.7 1.27074
    MYH8 Rooted myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 95.0526 85.3206 1.11406
    RPL3L Ranked 60s ribosomal protein l3-like. [swissprot;acc:q92901] 242.195 266.663 1.10103
    313 DYNLT1 Squared cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 71576.8 56326.7 1.27074
    MYH2 Rooted myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 95.0526 85.3206 1.11406
    PPP1R2 Measured protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 21644.2 18098.7 1.1959
    RRM2B Ranked ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 232.473 211.207 1.10069
    314 FZR1 Squared fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 71576.8 56326.7 1.27074
    METAP1 Ranked methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 1.10027
    MYH3 Rooted myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 95.0526 85.3206 1.11406
    PPP1R2P9 Measured type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 21632.5 18090 1.19583
    315 METAP2 Ranked 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] 244.126 268.604 1.10027
    MYH1 Rooted myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 95.0526 85.3206 1.11406
    PCSK5 Squared proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 71576.8 56326.7 1.27074
    RRS1 Measured ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 21370.8 17896.5 1.19413
    316 no value Rooted myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 95.0526 85.3206 1.11406
    EIF1 Ranked protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 267.017 1.10022

    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/