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 description Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1075 to 1124 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] POLR2L Divided 237.627 253.604 1.06724
    pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 Subtracted 58 44 14
    539 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] MYH2 112 126
    protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] MEMO1P Divided 236.964 252.86 1.06708
    540 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] PANK3 Subtracted 58 44 14
    selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 Divided 222.156 208.201 1.06703
    541 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] MICAL2
    myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] MYH3 Subtracted 112 126 14
    542 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] INPP4B Divided 222.156 208.201 1.06703
    myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] MYH1 Subtracted 112 126 14
    543 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] no value
    selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] SEPHS1 Divided 222.156 208.201 1.06703
    544 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] MYH7B Subtracted 112 126 14
    inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] INPP4A Divided 222.156 208.201 1.06703
    545 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] EIF6 248.866 233.287 1.06678
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Subtracted 58 44 14
    546 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] MYH13 112 126
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS Divided 207.222 194.262 1.06671
    547 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] AARS Subtracted 234.106 248.104 13.998
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK Divided 207.26 194.346 1.06645
    548 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 Subtracted 222.156 208.201 13.955
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2 Divided 207.26 194.346 1.06645
    549 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] MICAL2 Subtracted 222.156 208.201 13.955
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value Divided 207.26 194.346 1.06645
    550 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] INPP4B Subtracted 222.156 208.201 13.955
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Divided 207.26 194.346 1.06645
    551 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 207.261 194.347
    selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] SEPHS1 Subtracted 222.156 208.201 13.955
    552 crk-like protein. [swissprot;acc:p46109] CRKL Divided 207.26 194.346 1.06645
    inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] INPP4A Subtracted 222.156 208.201 13.955
    553 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Divided 207.26 194.346 1.06645
    putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] no value Subtracted 226.3 212.38 13.92
    554 proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Divided 207.26 194.346 1.06645
    t54 protein. [swissprot;acc:q92917] GPKOW Subtracted 226.3 212.38 13.92
    555 cbf1 interacting corepressor. [refseq;acc:nm_004882] no value 227.86 213.945 13.915
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR Divided 207.26 194.346 1.06645
    556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 207.27 194.368 1.06638
    evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] GPATCH1 Subtracted 227.86 213.945 13.915
    557 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Divided 207.272 194.371 1.06637
    shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] SBDS Subtracted 216.557 230.362 13.805
    558 tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] no value 248.994 235.255 13.739
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 135.087 144.041 1.06628
    559 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL 207.309 194.452 1.06612
    ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] RPP30 Subtracted 216.72 230.439 13.719
    560 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] SOS1 Divided 205.74 193.021 1.06589
    tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] DR1 Subtracted 232.118 218.406 13.712
    561 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] SOS2 Divided 205.89 193.183 1.06578
    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 Subtracted 228.215 214.546 13.669
    562 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] PRSS7 224.606 210.944 13.662
    ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] GULP1 Divided 220.744 207.121 1.06577

    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/