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 Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1625 to 1674 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    102 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Ranked Divided High confidence 88.2482 110.265 1.24949
    pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 Measured Subtracted Low confidence 10684.1 11611.2 927.1
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] CLP1 Squared High confidence 121200 85473.4 35726.6
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Measured Divided 2353.63 3225.65 1.3705
    protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] TGM1 Ranked Subtracted Low confidence 226.395 211.713 14.682
    rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP Rooted Divided High confidence 47.6504 36.9304 1.29028
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 Subtracted Low confidence 68.5063 74.6906 6.1843
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Measured Divided 5060.92 5567.34 1.10006
    103 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2
    cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 High confidence 2353.63 3225.65 1.3705
    cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Subtracted Low confidence 12315 11390.6 924.4
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 Rooted High confidence 19.9625 35.798 15.8355
    goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] COL4A3BP Ranked Low confidence 220.969 235.572 14.603
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] no value Squared Divided High confidence 407289 263351 1.54656
    natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] SLC11A2 Rooted Low confidence 64.1217 69.7 1.087
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 Squared Subtracted 62385.1 53596 8789.1
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS Rooted Divided High confidence 60.8365 77.7233 1.27758
    putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A Measured Subtracted 11068 8508.5 2559.5
    symplekin. [swissprot;acc:q92797] SYMPK Squared 124118 88668.8 35449.2
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Ranked 201.144 158.868 42.276
    trophinin. [swissprot;acc:q12816] TRO Divided 88.2482 110.265 1.24949
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] PTPRA Low confidence 203.948 189.652 1.07538
    vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] VPS33A Rooted Subtracted 69.1897 75.3346 6.1449
    zinc finger protein basonuclin. [swissprot;acc:q01954] BNC1 Squared Divided 105225 90141.3 1.16733
    104 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Ranked 219.277 204.212 1.07377
    associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Measured Subtracted High confidence 11068 8508.5 2559.5
    atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] ATP5O Squared Low confidence 61860.4 53172.3 8688.1
    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] CPSF4 Divided 60910.8 52263.5 1.16546
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 High confidence 407289 263351 1.54656
    diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] DGKH Rooted Subtracted Low confidence 62.2472 68.3765 6.1293
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Ranked Divided High confidence 252.371 202.016 1.24926
    jun dimerization protein. [refseq;acc:nm_130469] no value Rooted 60.8365 77.7233 1.27758
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T Squared Subtracted 121579 87259.3 34319.7
    musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 Measured Divided 4241.57 5810.79 1.36996
    natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] SLC11A1 Ranked Subtracted Low confidence 225.666 211.107 14.559
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 Measured 10665 11587.2 922.2
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 Rooted High confidence 19.9625 35.798 15.8355
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Measured Divided Low confidence 10618.8 11681.3 1.10006
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Ranked Subtracted High confidence 256.228 298.438 42.21
    vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] VPS18 Rooted Divided Low confidence 69.2771 75.2308 1.08594
    105 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 Ranked Subtracted 213.243 227.616 14.373
    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] CPSF4 Squared 60910.8 52263.5 8647.3
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Divided High confidence 407289 263351 1.54656
    diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] DGKD Rooted Subtracted Low confidence 62.2472 68.3765 6.1293
    fos-related antigen 2. [swissprot;acc:p15408] FOSL2 Divided High confidence 60.8675 77.7168 1.27682
    guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] GNB1 Ranked 266.716 333.165 1.24914
    monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] SLC16A2 Measured Subtracted Low confidence 10553.9 11452.8 898.9
    musashi 1. [refseq;acc:nm_002442] MSI1 Divided High confidence 4241.57 5810.79 1.36996
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Subtracted 11068 8508.5 2559.5
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 Squared Divided Low confidence 62385.1 53596 1.16399

    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/