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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
    Value Type	Ranked
    Rank description Network Comparison Type Interaction Map Filtered red green network_comparison 1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61] Divided High confidence 0 4294 15915 3.70633 1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976] Divided Low confidence 1 16 32 2 1 homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774] Subtracted High confidence 1 215 322 107 1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279] Subtracted Low confidence 1 223 330 107 1 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3] Subtracted High confidence 0 8906 21883 12977 1 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3] Subtracted Low confidence 0 8906 21883 12977 1 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849] Divided Low confidence 0 5865 14977 2.55362 1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172] Divided High confidence 1 10 24 2.4 2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61] Subtracted High confidence 0 4294 15915 11621 2 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802] Subtracted Low confidence 1 223 330 107 2 hbs1-like. [source:refseq;acc:nm_006620] Subtracted High confidence 1 215 322 107 2 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279] Divided Low confidence 1 223 330 1.47982 2 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476] Divided High confidence 1 15 28 1.86667 2 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3] Divided Low confidence 0 8906 21883 2.45711 2 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849] Divided High confidence 0 5865 14977 2.55362 2 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531] Subtracted Low confidence 0 9607 20617 11010 3 cab2. [source:refseq;acc:nm_033419] Subtracted High confidence 0 21866 10950 10916 3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802] Divided Low confidence 1 223 330 1.47982 3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534] Subtracted Low confidence 1 223 330 107 3 cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438] Divided High confidence 1 15 28 1.86667 3 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531] Divided Low confidence 0 9607 20617 2.14604 3 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721] Subtracted Low confidence 0 9607 20617 11010 3 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8] Divided High confidence 0 4475.84 11083.9 2.47638 3 rad50-interacting protein 1. [source:refseq;acc:nm_021930] Subtracted High confidence 1 337 232 105 4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534] Divided Low confidence 1 223 330 1.47982 4 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418] Divided High confidence 1 15 28 1.86667 4 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473] Subtracted Low confidence 1 223 330 107 4 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3] Divided High confidence 0 8906 21883 2.45711 4 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849] Subtracted Low confidence 0 5865 14977 9112 4 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721] Divided Low confidence 0 9607 20617 2.14604 4 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7] Subtracted High confidence 0 11525 21888 10363 4 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6] Subtracted High confidence 1 337 232 105 5 cytohesin 4. [source:swissprot;acc:q9uia0] Divided High confidence 1 15 28 1.86667 5 homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017] Subtracted Low confidence 0 22286 13216 9070 5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473] Divided Low confidence 1 223 330 1.47982 5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3] Subtracted Low confidence 1 318 240 78 5 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87] Subtracted High confidence 0 11525 21888 10363 5 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855] Divided High confidence 0 5510.5 11965.7 2.17144 5 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [source:swissprot;acc:o14607] Divided Low confidence 0 10889.4 19873 1.82499 5 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266] Subtracted High confidence 1 212 309 97 6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739] Divided High confidence 1 15 28 1.86667 6 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630] Subtracted Low confidence 0 22286 13216 9070 6 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849] Subtracted High confidence 0 5865 14977 9112 6 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5] Subtracted Low confidence 1 318 240 78 6 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3] Divided Low confidence 1 318 240 1.325 6 protein x 0004. [source:refseq;acc:nm_016301] Subtracted High confidence 1 212 309 97 6 trinucleotide repeat containing 15. [source:refseq;acc:nm_015575] Divided Low confidence 0 5575.71 9583.37 1.71877 6 ubiquitin protein ligase. [source:refseq;acc:nm_130466] Divided High confidence 0 7523 15339.2 2.03897 7 cab2. [source:refseq;acc:nm_033419] Divided High confidence 0 21866 10950 1.99689 7 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402] Divided Low confidence 0 11543 6812 1.69451 Legend: - Rank is the rank after comparing the two networks - 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/