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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1001 to 1050 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    126 Divided ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured 24250 18164.9 1.33499
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Rooted 60.9342 75.1387 1.23311
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 189976 124480 1.52616
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked 94 114 1.21277
    Subtracted AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared 71387.4 96033.4 24646
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked 285.684 252.234 33.45
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 14.1587
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Measured 450.5 2394.5 1944
    127 Divided no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 88432.6 58423.3 1.51365
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked 94 114 1.21277
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 1.23236
    JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 7523.39 1.33436
    Subtracted CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked 285.684 252.234 33.45
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 13.58
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared 71386.9 96032.5 24645.6
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Measured 450.5 2394.5 1944
    128 Divided no value pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 58155.8 1.50952
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 4355.61 5810.82 1.3341
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked 94 114 1.21277
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 1.23069
    Subtracted AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared 71346.6 95965.1 24618.5
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 252.234 33.45
    TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured 11004.2 12944.2 1940
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 67.9743 13.3216
    129 Divided LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 4358.13 5811.49 1.33348
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 66.7323 1.23044
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 178263 118639 1.50257
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked 94 114 1.21277
    Subtracted CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 33.45
    PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured 15274.9 13346.9 1928
    SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared 71062.4 95488.9 24426.5
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 67.9477 13.2852
    130 Divided no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 55.1026 67.5701 1.22626
    C10orf83 44050 protein. [refseq;acc:nm_178832] Squared 148058 99628.4 1.4861
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 94 114 1.21277
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured 2234.68 2978.53 1.33287
    Subtracted CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] Squared 71062.4 95488.9 24426.5
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked 242.735 276.059 33.324
    GATAD2A p66 alpha. [refseq;acc:nm_017660] Measured 12839 10911.1 1927.9
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Rooted 144.606 157.824 13.218
    131 Divided no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 55.1113 67.5537 1.22577
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured 2234.73 2978.57 1.33285
    PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Squared 148058 99628.4 1.4861
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked 294.053 242.562 1.21228
    Subtracted no value succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Squared 71062.4 95488.9 24426.5
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 276.018 33.3
    GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1927.9
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Rooted 144.606 157.824 13.218
    132 Divided ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared 36359.2 24466.8 1.48606
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured 2236.61 2980.35 1.33253

    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/