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 description Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    199 serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Divided PPP2CA Measured High confidence 4916.8 3888.18 1.26455
    single-stranded dna-binding protein 4. [swissprot;acc:q9bwg4] Subtracted SSBP4 Squared Low confidence 52164.3 47095.3 5069
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided STT3B Rooted High confidence 61.2893 70.3856 1.14842
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] PRSS16 Squared 71062.2 95488.6 1.34373
    tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] TPM4 Rooted Low confidence 70.8512 75.1709 1.06097
    200 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted no value Ranked High confidence 241.808 267.335 25.527
    60s ribosomal protein l27. [swissprot;acc:p08526] Divided RPL27 Rooted Low confidence 69.691 73.939 1.06095
    alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] CRYAB Ranked 219.543 208.868 1.05111
    anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Subtracted ANAPC10 213.495 203.244 10.251
    aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] AQP1 Measured High confidence 10635.3 12111.4 1476.1
    bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Divided BRD3 Squared Low confidence 54179.7 48910.9 1.10772
    cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] Subtracted TMED2 Measured 9810.95 10381.3 570.35
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided BCAR1 High confidence 4808.79 6074.21 1.26315
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] EGFL7 Ranked 242.718 276.018 1.1372
    gk001 protein. [refseq;acc:nm_020198] CCDC47 Squared 71062.2 95488.6 1.34373
    mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Subtracted MAPKAPK3 42411.6 55802.1 13390.5
    nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] NOX1 Rooted Low confidence 69.9166 74.219 4.3024
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided STT3A High confidence 61.2893 70.3856 1.14842
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 Measured Low confidence 6926.74 7434.04 1.07324
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted PPP2CA Rooted High confidence 63.5827 53.0856 10.4971
    tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] TNXB Squared Low confidence 52164 47095.1 5068.9
    201 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 Ranked High confidence 241.828 267.346 25.518
    a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Divided ARAF Measured Low confidence 10392.7 9683.56 1.07323
    aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Subtracted AKR7A3 9249.74 9818.95 569.21
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Divided CLSTN2 Squared High confidence 71033.4 95440.2 1.3436
    cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Subtracted CPSF4 Rooted 138.375 127.926 10.449
    cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Divided CYC1 Ranked Low confidence 208.591 219.23 1.051
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Rooted 71.1262 75.4476 1.06076
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] DDOST High confidence 61.2893 70.3856 1.14842
    hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] HEY1 Squared Low confidence 52176.8 47103.2 1.10771
    mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Subtracted MAPK14 High confidence 42411.6 55802.1 13390.5
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Rooted Low confidence 70.4583 74.7299 4.2716
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided SF4 Ranked High confidence 240.133 211.382 1.13601
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 Measured 4810.22 6075.04 1.26294
    tenascin n precursor (fragment). [sptrembl;acc:q9uqp3] Subtracted TNN Squared Low confidence 52163.9 47095 5068.9
    translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] SSR4 Measured High confidence 10603.5 12069.5 1466
    ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] UBE2E1 Ranked Low confidence 203.935 214.089 10.154
    202 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided NCBP2 Rooted 71.0652 75.377 1.06067
    40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted RPS4Y2 Ranked High confidence 240.758 266.079 25.321
    aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] AKR7A2 Measured Low confidence 9246.23 9814.59 568.36
    calsyntenin-1 precursor. [swissprot;acc:o94985] CLSTN1 High confidence 10603.5 12069.5 1466
    calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Divided CLSTN3 Squared 71030.1 95434.8 1.34358
    dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Subtracted XKR7 Ranked Low confidence 178.507 168.371 10.136
    enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Divided NEDD9 Measured High confidence 4812.01 6076.09 1.26269
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] GNG4 Ranked Low confidence 211.51 222.252 1.05079
    neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Subtracted CHRNA4 Squared High confidence 42411.6 55802.1 13390.5
    phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Divided PGM3 Low confidence 55537.3 50139.7 1.10765
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Measured 10391.8 9682.99 1.0732
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] TRPC4 Ranked High confidence 201.478 228.784 1.13553
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted SNRPD1 Rooted Low confidence 71.0886 75.3451 4.2565

    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/