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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1230 to 1279 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		network_comparison
    		green
    308 DENR Rooted density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 50.4687 1.11476 45.2733
    DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 4977.09 1.19878 5966.44
    RPL34 Ranked 60s ribosomal protein l34. [swissprot;acc:p49207] 242.153 1.10126 266.673
    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 1.11424 62.6036
    CUTL1 Squared ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 28900.8 1.27203 36762.6
    DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 4977.8 1.19855 5966.14
    SEC61A2 Ranked protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 242.153 1.10126 266.673
    310 no value Rooted myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 95.0526 1.11406 85.3206
    CUTL2 Squared homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 28901.4 1.27198 36762.1
    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 1.19736 5878.79
    SEC61A1 Ranked protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 1.10126 266.673
    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 1.27154 38866.5
    DVL3 Measured segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 4981.52 1.19734 5964.58
    EIF1B Ranked protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 242.627 1.10108 267.151
    MYH4 Rooted myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 95.0526 1.11406 85.3206
    312 no value Measured u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 4598.21 1.19622 5500.48
    Squared methyltransferase like 2. [refseq;acc:nm_018396] 71576.8 1.27074 56326.7
    MYH8 Rooted myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 95.0526 1.11406 85.3206
    RPL3L Ranked 60s ribosomal protein l3-like. [swissprot;acc:q92901] 242.195 1.10103 266.663
    313 DYNLT1 Squared cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 71576.8 1.27074 56326.7
    MYH2 Rooted myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 95.0526 1.11406 85.3206
    PPP1R2 Measured protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 21644.2 1.1959 18098.7
    RRM2B Ranked ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 232.473 1.10069 211.207
    314 FZR1 Squared fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 71576.8 1.27074 56326.7
    METAP1 Ranked methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 1.10027 268.604
    MYH3 Rooted myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 95.0526 1.11406 85.3206
    PPP1R2P9 Measured type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 21632.5 1.19583 18090
    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 1.10027 268.604
    MYH1 Rooted myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 95.0526 1.11406 85.3206
    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 1.27074 56326.7
    RRS1 Measured ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 21370.8 1.19413 17896.5
    316 no value Rooted myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 95.0526 1.11406 85.3206
    EIF1 Ranked protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 1.10022 267.017
    PPP1CA Measured serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 21370.8 1.19413 17896.5
    WASL Squared neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 28918.3 1.27068 36746
    317 no value Ranked splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 224.445 1.09998 204.044
    ADIPOR2 Measured adiponectin receptor 2. [refseq;acc:nm_024551] 3153.1 1.19329 3762.56
    MYH7B Rooted dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 95.0526 1.11406 85.3206
    NME3 Squared nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 33982.3 1.27005 43159.1
    318 no value Measured nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 34190.9 1.19318 40795.8
    MRPL3 Ranked mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 1.09987 266.18
    MYH13 Rooted myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 95.0526 1.11406 85.3206
    TOMM20 Squared mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 46739.9 1.26518 59134.5
    319 NIP7 Rooted saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 49.0663 1.1107 54.4978
    PEX19 Squared peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 46739.9 1.26518 59134.5
    RPL19 Ranked 60s ribosomal protein l19. [swissprot;acc:p14118] 240.73 1.09969 264.729
    RRAGA Measured ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 20911 1.19117 24908.5
    320 no value Rooted 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 1.11005 45.294
    CDH1 Ranked epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 1.0995 265.96
    EPHX1 Squared epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 87971.9 1.26463 69563.1

    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/