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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 723 to 772 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    723 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] no value 244.842 232.577 1.05274
    724 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
    725 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] MVK 235.296 247.673 1.0526
    726 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] FTSJ3 244.495 232.419 1.05196
    727 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] NUAK1 208.873 219.71 1.05188
    728 n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] B3GNT1 208.874 219.708 1.05187
    729 huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] no value
    730 mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] TIMM10
    731 fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] FH
    732 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 124.434 118.318 1.05169
    733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL 164 155.961 1.05154
    734 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] no value 232.601 244.534 1.0513
    735 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] RANP1
    736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] no value
    737 septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 125.526 119.402 1.05129
    738 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] XAB2 222.825 211.966 1.05123
    739 phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] PFAS 223.58 235.027 1.0512
    740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] ATIC
    741 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] PAICS
    742 brain protein 44. [swissprot;acc:o95563] BRP44 126.215 120.078 1.05111
    743 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7
    744 septin 6. [swissprot;acc:q14141] SEPT6 126.604 120.463 1.05098
    745 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] SLC35B1 214.679 225.568 1.05072
    746 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] EIF3I 250.465 238.38 1.0507
    747 trinucleotide repeat containing 15. [refseq;acc:nm_015575] no value
    748 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] FBL 245.246 233.483 1.05038
    749 exocyst complex component sec15b. [swissprot;acc:q9y2d4] EXOC6B 221.968 211.326 1.05036
    750 exocyst complex component sec15a. [swissprot;acc:q8tag9] EXOC6 222.138 211.503 1.05028
    751 u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] no value 223.463 212.875 1.04974
    752 step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7
    753 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] LBP 224.434 235.583 1.04968
    754 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] SPCS2
    755 uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] UMPS
    756 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] CLPTM1
    757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] BPI
    758 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] PLTP
    759 osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 231.809 243.289 1.04952
    760 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 246.055 234.458 1.04946
    761 signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB 213.325 203.303 1.0493
    762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 213.256 203.237
    763 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] N6AMT1 228.78 218.091 1.04901
    764 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] PRPF3 222.082 211.707
    765 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] HEMK1 229.045 218.343
    766 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] TRIOBP 213.804 224.226 1.04875
    767 rho interacting protein 3. [refseq;acc:nm_015134] no value 213.803 224.224 1.04874
    768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 210.946 221.225 1.04873
    769 cab2. [refseq;acc:nm_033419] PERLD1
    770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5
    771 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] DNAJB1
    772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] ETF1

    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/