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 [...,...].
    Gene Rank Value Type Hugo Network Comparison Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 66312 in total
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    199 Squared SSBP4 Subtracted single-stranded dna-binding protein 4. [swissprot;acc:q9bwg4] Low confidence 5069 52164.3 47095.3
    Rooted LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] High confidence 10.6266 55.297 65.9236
    NOX3 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence 4.3024 69.9164 74.2188
    STT3B Divided source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] High confidence 1.14842 61.2893 70.3856
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Low confidence 1.06097 70.8512 75.1709
    200 Measured AQP1 Subtracted 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 1476.1 10635.3 12111.4
    BCAR1 Divided crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 1.26315 4808.79 6074.21
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 1.07324 6926.74 7434.04
    TMED2 Subtracted cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] 570.35 9810.95 10381.3
    Ranked no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] High confidence 25.527 241.808 267.335
    ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Low confidence 10.251 213.495 203.244
    CRYAB Divided alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] 1.05111 219.543 208.868
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] High confidence 1.1372 242.718 276.018
    Squared BRD3 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Low confidence 1.10772 54179.7 48910.9
    CCDC47 gk001 protein. [refseq;acc:nm_020198] High confidence 1.34373 71062.2 95488.6
    MAPKAPK3 Subtracted mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 13390.5 42411.6 55802.1
    TNXB tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] Low confidence 5068.9 52164 47095.1
    Rooted NOX1 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 4.3024 69.9166 74.219
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence 10.4971 63.5827 53.0856
    RPL27 Divided 60s ribosomal protein l27. [swissprot;acc:p08526] Low confidence 1.06095 69.691 73.939
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 1.14842 61.2893 70.3856
    201 Measured AKR7A3 Subtracted aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Low confidence 569.21 9249.74 9818.95
    ARAF Divided a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 1.07323 10392.7 9683.56
    CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 1.26294 4810.22 6075.04
    SSR4 Subtracted translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 1466 10603.5 12069.5
    Ranked CYC1 Divided cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Low confidence 1.051 208.591 219.23
    RPL11 Subtracted 60s ribosomal protein l11. [swissprot;acc:p39026] High confidence 25.518 241.828 267.346
    SF4 Divided splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1.13601 240.133 211.382
    UBE2E1 Subtracted ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Low confidence 10.154 203.935 214.089
    Squared CLSTN2 Divided calsyntenin-2 precursor. [swissprot;acc:q9h4d0] High confidence 1.3436 71033.4 95440.2
    HEY1 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] Low confidence 1.10771 52176.8 47103.2
    MAPK14 Subtracted 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] High confidence 13390.5 42411.6 55802.1
    TNN tenascin n precursor (fragment). [sptrembl;acc:q9uqp3] Low confidence 5068.9 52163.9 47095
    Rooted CPSF4 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] High confidence 10.449 138.375 127.926
    DDOST Divided 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] 1.14842 61.2893 70.3856
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Low confidence 1.06076 71.1262 75.4476
    STT3A Subtracted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 4.2716 70.4583 74.7299
    202 Measured AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 568.36 9246.23 9814.59
    CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] High confidence 1466 10603.5 12069.5
    NEDD9 Divided 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] 1.26269 4812.01 6076.09
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Low confidence 1.0732 10391.8 9682.99
    Ranked GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 1.05079 211.51 222.252
    RPS4Y2 Subtracted 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 25.321 240.758 266.079
    TRPC4 Divided short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1.13553 201.478 228.784
    XKR7 Subtracted dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 10.136 178.507 168.371
    Squared CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] High confidence 13390.5 42411.6 55802.1
    CLSTN3 Divided calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 1.34358 71030.1 95434.8
    PGM3 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Low confidence 1.10765 55537.3 50139.7
    TNR Subtracted tenascin r (restrictin, janusin). [refseq;acc:nm_003285] 5068.9 52163.9 47095
    Rooted no value Divided splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] High confidence 1.14724 57.3527 65.7973

    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/