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 description Rank Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 401 to 450 of 473 in total
    Value Type  : Ranked
    Network Comparison Type  : Subtracted
    Interaction Map  : High confidence
    red  : 0
    Filtered  : 1
    green  : 0
    network_comparison  : 0
    description
    		Rank
    		Hugo
    transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] 2969 TFAP2A
    transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] 3220 TFAP2B
    transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754] 3164 TFAP2C
    transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923] 3182 TCF3
    transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444] 2792 MAF
    transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3] 2790 no value
    transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3] 2778 MAFA
    transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [swissprot;acc:q9uh92] 3091 MLX
    transcription initiation factor iia alpha and beta chains (tfiia p35 and p19 subunits) (tfiia-42) (tfiial). [swissprot;acc:p52655] 2848 GTF2A1
    transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657] 2946 GTF2A2
    transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [swissprot;acc:p29083] 2894 GTF2E1
    transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 3178 no value
    transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] 2941 TAF4B
    transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 2999 TAF4
    transcription initiation factor tfiid 30 kda subunit (tafii-30) (tafii30). [swissprot;acc:q12962] 2839 TAF10
    transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594] 3043 TTF2
    transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [refseq;acc:nm_057175] 2854 NARG1
    transcriptional repressor nac1. [refseq;acc:nm_052876] 2872 BTBD14B
    transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [swissprot;acc:q12986] 3169 NFX1
    transforming growth factor beta 1 precursor (tgf-beta 1). [swissprot;acc:p01137] 3105 TGFB1
    transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [swissprot;acc:p08112] 3155 TGFB2
    transforming growth factor beta 3 precursor (tgf-beta 3). [swissprot;acc:p10600] 3035 TGFB3
    transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45] 3174 TM9SF3
    transmembrane protein 4. [refseq;acc:nm_014255] 2923 TMEM4
    transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766] 3041 TTR
    trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494] 3159 TNRC6A
    tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] 2945 TPM1
    tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 2931 TPM3
    tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] 2833 TPM4
    tu12b1-ty protein. [refseq;acc:nm_016575] 3074 NT5DC3
    tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [swissprot;acc:p05214] 3175 TUBA3D
    tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922] 3141 TTLL1
    tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347] 2817 TBCA
    tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] 2858 RYK
    ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995] 3192 USP13
    ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974] 3075 USP5
    ubiquitin protein ligase. [refseq;acc:nm_130466] 2902 UBE3B
    ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 2828 no value
    ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] 3094 UBE2S
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] 3001 NEDD8
    udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] 2810 UGT2A1
    udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224] 2835 UGT1A9
    udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 3085 UGT2B10
    udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 2819 no value
    udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 3086
    udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 2793
    udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [swissprot;acc:q9by64] 2979 UGT2B28
    udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 2889 UGT2B4
    udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662] 2818 UGT2B7
    uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 3030 C6orf35

    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/