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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1714 to 1763 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    215 FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Rooted Low confidence 69.3328 73.4772 1.05978
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured High confidence 16074 12888.4 1.24717
    LIPA lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared Low confidence 54531.1 49322.8 1.1056
    NCDN neurochondrin. [refseq;acc:nm_014284] Measured 10492.4 9804.73 1.07014
    NEGR1 a kindred of iglon. [refseq;acc:nm_173808] Ranked 199.671 209.654 1.05
    PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared High confidence 86609.4 65234.5 1.32766
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 92.2415 1.14054
    216 CDC14C cdc14 homolog b isoform 2. [refseq;acc:nm_033331] Squared Low confidence 53433.9 48332.8 1.10554
    FMO2 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Rooted 69.3306 73.4747 1.05977
    MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Ranked High confidence 112 126 1.125
    NMBR neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336] Low confidence 199.671 209.654 1.05
    PPP1R12A protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Measured 8973.23 9597.94 1.06962
    PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared High confidence 86600.9 65229.9 1.32763
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Measured 16071.6 12886.8 1.24714
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 105.205 92.2415 1.14054
    217 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Measured 16071.6 12886.8 1.24714
    BRD2 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] Squared Low confidence 53878.5 48740.6 1.10541
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Rooted High confidence 105.205 92.2415 1.14054
    FMO1 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Low confidence 69.3362 73.4783 1.05974
    GRPR gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [swissprot;acc:p30550] Ranked 199.671 209.654 1.05
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] High confidence 112 126 1.125
    PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Squared 86600.9 65229.9 1.32763
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Measured Low confidence 7633.16 8153.06 1.06811
    218 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Rooted High confidence 46.1476 52.5742 1.13926
    BRS3 bombesin receptor subtype-3 (brs-3). [swissprot;acc:p32247] Ranked Low confidence 199.671 209.654 1.05
    FMO4 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Rooted 69.3373 73.4787 1.05973
    HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Measured High confidence 16070.4 12886 1.24712
    LIPM ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared Low confidence 54471.8 49292.4 1.10508
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Ranked High confidence 112 126 1.125
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Measured Low confidence 7266.93 7759.2 1.06774
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Squared High confidence 86600.9 65229.9 1.32763
    219 no value f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Rooted Low confidence 68.4447 72.5017 1.05927
    transforming protein n-ras. [swissprot;acc:p01111] Measured High confidence 16069.8 12885.6 1.24711
    BACH1 transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Ranked Low confidence 172.647 164.44 1.04991
    BRDT testis-specific bromodomain protein. [refseq;acc:nm_001726] Squared 53732.5 48658.1 1.10429
    COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] High confidence 86600.9 65229.9 1.32763
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Ranked 112 126 1.125
    RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Rooted 52.7146 60.0088 1.13837
    SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Measured Low confidence 7653.44 8171.53 1.06769
    220 no value 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). [swissprot;acc:o60476] High confidence 41482.5 33356.5 1.24361
    COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Squared 86600.9 65229.9 1.32763
    LIPF triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Low confidence 54309.4 49192.4 1.10402
    MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Rooted High confidence 52.7557 60.035 1.13798
    MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Ranked 112 126 1.125
    NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] Measured Low confidence 9395.91 10028.6 1.06734
    NFE2L2 nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Ranked 172.647 164.44 1.04991
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Rooted 68.7644 72.8317 1.05915
    221 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Ranked High confidence 112 126 1.125
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured Low confidence 10491.4 9831.19 1.06715
    BACH2 transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Ranked 172.647 164.44 1.04991

    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/