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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 55524 to 55573 of 66312 in total
    Network Comparison Type  : Subtracted
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    2796 Rooted dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] High confidence DMAP1 0 0 0
    2797 Measured neurocalcin delta. [swissprot;acc:p29554] Low confidence NCALD 230.9 7964.19 8195.09
    sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280] High confidence ODF3 0 0 0
    Ranked
    wd repeat domain 23 isoform 1. [refseq;acc:nm_025230] Low confidence WDR23 3.425 199.627 196.202
    Squared dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] no value 1578.1 46593.5 45015.4
    sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280] High confidence ODF3 0 0 0
    Rooted nadh-ubiquinone oxidoreductase subunit b14.5b (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14.5b) (ci-b14.5b). [swissprot;acc:o95298] Low confidence NDUFC2 2.3566 73.0118 75.3684
    sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280] High confidence ODF3 0 0 0
    2798 Measured ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] ARIH2
    lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Low confidence LIN7B 230.88 7659.58 7890.46
    Ranked ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] High confidence ARIH2 0 0 0
    atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] Low confidence XRCC5 3.425 200.069 196.644
    Squared ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] High confidence ARIH2 0 0 0
    phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Low confidence PAH 1578 44110.6 42532.6
    Rooted ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] High confidence ARIH2 0 0 0
    phosphatidylinositol 4-kinase, catalytic, beta polypeptide. [refseq;acc:nm_002651] Low confidence PI4KB 2.3566 72.8397 75.1963
    2799 Measured hmg2 like. [refseq;acc:nm_145205] High confidence HMGB4 0 0 0
    wd-repeat protein 4. [swissprot;acc:p57081] Low confidence WDR4 230.83 7906.09 8136.92
    Ranked hmg2 like. [refseq;acc:nm_145205] High confidence HMGB4 0 0 0
    ndrg3 protein. [swissprot;acc:q9ugv2] Low confidence HNRPA3P2 3.424 202.793 199.369
    Squared hmg2 like. [refseq;acc:nm_145205] High confidence HMGB4 0 0 0
    rd protein. [swissprot;acc:p18615] Low confidence no value 1578 44110.6 42532.6
    Rooted 28s ribosomal protein s18c, mitochondrial precursor (mrp-s18-c) (mrps18c) (mrp-s18-1) (cgi-134). [swissprot;acc:q9y3d5] MRPS18C 2.3563 72.2922 74.6485
    hmg2 like. [refseq;acc:nm_145205] High confidence HMGB4 0 0 0
    2800 Measured mondoa. [refseq;acc:nm_014938] MLXIP
    phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937] Low confidence PIGT 230.77 7913.16 8143.93
    Ranked mondoa. [refseq;acc:nm_014938] High confidence MLXIP 0 0 0
    poly(a) binding protein, nuclear 1; oculopharyngeal muscular dystrophy; poly(a)-binding protein, nuclear 1; poly(a) binding protein ii; poly(a) binding protein 2. [refseq;acc:nm_004643] Low confidence PABPN1 3.424 204.908 201.484
    Squared j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 1578 44110.6 42532.6
    mondoa. [refseq;acc:nm_014938] High confidence MLXIP 0 0 0
    Rooted fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] Low confidence ZFYVE20 2.3563 72.2922 74.6485
    mondoa. [refseq;acc:nm_014938] High confidence MLXIP 0 0 0
    2801 Measured dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] ERCC4
    sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Low confidence SRPK1 230.77 8020.09 8250.86
    Ranked dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] High confidence ERCC4 0 0 0
    dolichyl-p-mannose:man7glcnac2-pp-dolichyl mannosyltransferase. [refseq;acc:nm_024105] Low confidence ALG12 3.421 200.078 196.657
    Squared dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] High confidence ERCC4 0 0 0
    musashi 1. [refseq;acc:nm_002442] Low confidence MSI1 1577.5 46584.1 45006.6
    Rooted dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] High confidence ERCC4 0 0 0
    guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Low confidence GUK1 2.3558 72.1834 74.5392
    2802 Measured 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] High confidence no value 0 0 0
    serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Low confidence SRPK3 230.76 8022.82 8253.58
    Ranked 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] High confidence no value 0 0 0
    craniofacial development protein 1; phosphoprotein (bucentaur). [refseq;acc:nm_006324] Low confidence CFDP1 3.421 200.078 196.657
    Squared 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] High confidence no value 0 0 0
    phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Low confidence PIK3C2B 1577.2 44752.7 43175.5
    Rooted 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] High confidence no value 0 0 0
    transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Low confidence TBL2 2.3557 71.2336 73.5893
    2803 Measured nanos (fragment). [sptrembl;acc:q8wy41] High confidence no value 0 0 0

    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/