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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2951 to 3000 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    738 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] no value Squared 31467.1 36752.2 1.16796
    xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] XAB2 Ranked 222.825 211.966 1.05123
    739 cellular modulator of immune recognition. [refseq;acc:nm_145021] MARCH8 Measured 5768.32 6434.78 1.11554
    exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] EXOC5 Rooted 65.3677 69.828 1.06823
    phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] PFAS Ranked 223.58 235.027 1.0512
    ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] RNASEH2A Squared 25727.7 30046.7 1.16787
    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 Ranked 223.58 235.027 1.0512
    casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] CSNK2A1P Rooted 53.1114 56.7251 1.06804
    o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] OSGEP Squared 22075.1 25775.1 1.16761
    vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] ATP6V0B Measured 5768.32 6434.78 1.11554
    741 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] CSNK2A2 Rooted 53.1114 56.7251 1.06804
    gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] SGCG Measured 5768.32 6434.78 1.11554
    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 Ranked 223.58 235.027 1.0512
    nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Squared 23894.7 27894.5 1.16739
    742 brain protein 44. [swissprot;acc:o95563] BRP44 Ranked 126.215 120.078 1.05111
    eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] EIF3G Measured 4131.04 4607.9 1.11543
    homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] EN2 Squared 31406.6 36662.8 1.16736
    transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] BTF3 Rooted 67.0234 71.5506 1.06755
    743 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] CXXC1 Squared 31406.6 36662.8 1.16736
    eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] EIF3A Measured 4131.04 4607.9 1.11543
    katanin p60 subunit a 1. [refseq;acc:nm_007044] KATNA1 Rooted 54.4988 51.0573 1.0674
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Ranked 126.215 120.078 1.05111
    744 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] ABT1 Squared 31406.6 36662.8 1.16736
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 Measured 12515.4 11221.1 1.11535
    dynactin 4. [refseq;acc:nm_032486] DCTN5 Rooted 55.2242 51.7372 1.0674
    septin 6. [swissprot;acc:q14141] SEPT6 Ranked 126.604 120.463 1.05098
    745 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] no value Squared 31406.6 36662.8 1.16736
    neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] NET1 Measured 4086.6 4557.68 1.11527
    solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] SLC35B1 Ranked 214.679 225.568 1.05072
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] no value Rooted 67.0475 71.5566 1.06725
    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 Ranked 250.465 238.38 1.0507
    hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] HECW1 Squared 31406.6 36662.8 1.16736
    katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] KATNB1 Rooted 54.5195 51.084 1.06725
    rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] ARHGEF3 Measured 4086.6 4557.68 1.11527
    747 down-regulated in metastasis. [refseq;acc:nm_014503] UTP20
    sr rich protein. [refseq;acc:nm_032870] SFRS18 Rooted 61.4809 65.6088 1.06714
    transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] TLE3 Squared 31401.8 36655.7 1.16731
    trinucleotide repeat containing 15. [refseq;acc:nm_015575] no value Ranked 250.465 238.38 1.0507
    748 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] BCAS2 Squared 23148.8 27021.5 1.1673
    ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS Measured 12503.3 11212 1.11517
    fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] FBL Ranked 245.246 233.483 1.05038
    mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] PMPCB Rooted 60.4376 64.4898 1.06705
    749 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 66.9737 71.4637 1.06704
    cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] CDC5L Squared 23148.8 27021.5 1.1673
    ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] PCYT2 Measured 4565.34 5085.92 1.11403
    exocyst complex component sec15b. [swissprot;acc:q9y2d4] EXOC6B Ranked 221.968 211.326 1.05036
    750 exocyst complex component sec15a. [swissprot;acc:q8tag9] EXOC6 222.138 211.503 1.05028
    mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] PMPCA Rooted 60.4385 64.49 1.06704
    myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] MYL1 Measured 4565.34 5085.92 1.11403
    n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] NAT5 Squared 21678.4 25303.3 1.16721

    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/