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 3051 to 3100 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    191 PXK px serine/threonine kinase. [refseq;acc:nm_017771] Ranked Subtracted Low confidence 196.372 206.947 10.575
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Measured 10730.1 10148.2 581.9
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided High confidence 4638.1 5923.4 1.27712
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked Low confidence 201.43 191.43 1.05224
    SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared Subtracted High confidence 42411.6 55802.1 13390.5
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Rooted Low confidence 70.8512 75.1709 4.3197
    192 no value bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Ranked 196.372 206.947 10.575
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured High confidence 10807.4 12338.5 1531.1
    AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared Divided 71387.4 96033.4 1.34524
    ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured 17757.5 14008 1.26767
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted Low confidence 5674.92 6255.18 580.26
    DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Squared High confidence 42411.6 55802.1 13390.5
    DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Rooted Low confidence 69.8853 74.201 4.3157
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Squared 51551.5 46457.1 5094.4
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked High confidence 241.373 267.352 25.979
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 199.458 1.14055
    NOX5 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Rooted Low confidence 69.9161 74.2187 1.06154
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted High confidence 116.792 106.107 10.685
    RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Ranked Divided Low confidence 217.341 206.571 1.05214
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Rooted High confidence 53.6107 61.5862 1.14877
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Squared Low confidence 51506.6 46445.8 1.10896
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 9385.4 10086.4 1.07469
    193 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Subtracted 5752.65 6330.03 577.38
    DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared High confidence 42411.6 55802.1 13390.5
    DUOX1 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Rooted Low confidence 69.8912 74.2044 4.3132
    HBS1L hbs1-like. [refseq;acc:nm_006620] Ranked Divided 206.166 216.913 1.05213
    HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Squared Subtracted 52187.1 47109.7 5077.4
    HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Divided 51484.4 46440.2 1.10862
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] High confidence 71386.9 96032.5 1.34524
    MSI1 musashi 1. [refseq;acc:nm_002442] Ranked 227.491 199.458 1.14055
    NOSTRIN nostrin. [refseq;acc:nm_052946] Rooted 59.6399 51.9242 1.1486
    NOX4 nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 69.9166 74.219 1.06154
    PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked Subtracted High confidence 241.373 267.352 25.979
    PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Measured 4612.39 3093.6 1518.79
    PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Rooted 116.707 106.044 10.663
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured Divided 17756.5 14007.3 1.26766
    STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence 6534.34 7021.2 1.07451
    TSGA10 testis specific, 10. [refseq;acc:nm_025244] Ranked Subtracted 196.373 206.946 10.573
    194 no value transforming protein n-ras. [swissprot;acc:p01111] Squared Divided 51474.3 46437.7 1.10846
    AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] High confidence 71346.6 95965.1 1.34505
    BRDT testis-specific bromodomain protein. [refseq;acc:nm_001726] Subtracted Low confidence 53732.5 48658.1 5074.4
    CCNG2 cyclin g2. [swissprot;acc:q16589] Measured Divided High confidence 17738.6 13995.7 1.26743
    Rooted Subtracted 116.707 106.044 10.663
    COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked Divided Low confidence 215.723 205.046 1.05207
    MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared Subtracted High confidence 42411.6 55802.1 13390.5
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted Low confidence 71.0652 75.377 4.3118
    NOX3 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Divided 69.9164 74.2188 1.06154
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked Subtracted High confidence 241.373 267.352 25.979
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Measured 4300.47 5807.72 1507.25
    RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Ranked Low confidence 183.27 172.702 10.568

    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/