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 network_comparison green
    Results: HTML CSV LaTeX Showing element 980 to 1029 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		red
    		network_comparison
    		green
    123 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided TIA1 Rooted 54.6527 1.24375 67.9743
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 Ranked 269.23 1.21681 327.601
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted FOSB Measured 4942.49 2094.83 7037.32
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided PPP1R2 Squared 192904 1.52896 126167
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted SNRPD1 Ranked 227.032 33.976 193.056
    124 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] AQP4 Squared 71389.9 24647.7 96037.6
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] NFYA Rooted 46.7419 14.1918 60.9337
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Measured 4944.3 2093.74 7038.04
    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] Divided HMG20B Ranked 208.52 1.21519 171.595
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Measured 24255.7 1.33501 18168.9
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 Rooted 54.6625 1.24304 67.9477
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted PSEN2 Ranked 285.684 33.45 252.234
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Divided PPP1R2P9 Squared 192779 1.52884 126095
    125 aquaporin 5. [swissprot;acc:p55064] Subtracted AQP5 71388.5 24646.7 96035.2
    high-mobility group 20a. [refseq;acc:nm_018200] Divided HMG20A Ranked 208.588 1.21429 171.778
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted NFU1 Measured 12471.7 2090 14561.7
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided MAP1LC3A 24255.7 1.33501 18168.9
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 Squared 189976 1.52616 124480
    s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted SKP1A Ranked 285.684 33.45 252.234
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided SNRPD1 Rooted 54.8203 1.23921 67.934
    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] Subtracted SON 35.6294 14.1825 49.8119
    126 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] AQP2 Squared 71387.4 24646 96033.4
    associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided STAMBPL1 Ranked 94 1.21277 114
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Measured 24250 1.33499 18164.9
    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] Subtracted FBXW7 Ranked 285.684 33.45 252.234
    high-mobility group 20a. [refseq;acc:nm_018200] HMG20A Rooted 60.9353 14.1587 75.094
    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] Divided HMG20B 60.9342 1.23311 75.1387
    rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted RINT1 Measured 450.5 1944 2394.5
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided PPP1CA Squared 189976 1.52616 124480
    127 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Subtracted CUL2 Ranked 285.684 33.45 252.234
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Divided no value Squared 88432.6 1.51365 58423.3
    deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted DNASE2B Rooted 153.191 13.58 166.771
    high-mobility group 20a. [refseq;acc:nm_018200] Divided HMG20A 60.9353 1.23236 75.094
    lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Subtracted MIP Squared 71386.9 24645.6 96032.5
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided CHMP2A Ranked 94 1.21277 114
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Subtracted RHOBTB2 Measured 450.5 1944 2394.5
    transcription factor jun-d. [swissprot;acc:p17535] Divided JUND 5638.2 1.33436 7523.39
    128 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Subtracted AQP1 Squared 71346.6 24618.5 95965.1
    associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided STAMBP Ranked 94 1.21277 114
    luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] LUC7L2 Measured 4355.61 1.3341 5810.82
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Subtracted TIA1 Rooted 54.6527 13.3216 67.9743
    pnas-18. [sptrembl;acc:q9bzu3] Divided no value Squared 87787.3 1.50952 58155.8
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted PSEN1 Ranked 285.684 33.45 252.234
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 Measured 11004.2 1940 12944.2
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided TARDBP Rooted 48.0515 1.23069 39.0445
    129 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted CUL1 Ranked 285.684 33.45 252.234
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided NCBP2L Rooted 54.2343 1.23044 66.7323
    luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] LUC7L Measured 4358.13 1.33348 5811.49
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Ranked 94 1.21277 114
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted TIAL1 Rooted 54.6625 13.2852 67.9477

    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/