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 Hugo Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1630 to 1679 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    102 STAMBPL1 Subtracted Measured associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 11068 8508.5 2559.5
    TEX28P2 Divided testis-specific protein tex28. [swissprot;acc:o15482] Low confidence 5060.92 5567.34 1.10006
    TGM1 Subtracted Ranked protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] 226.395 211.713 14.682
    103 no value Divided Squared 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] High confidence 407289 263351 1.54656
    BNC1 zinc finger protein basonuclin. [swissprot;acc:q01954] Low confidence 105225 90141.3 1.16733
    CHMP2A Subtracted Measured putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] High confidence 11068 8508.5 2559.5
    COL4A3BP Ranked 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] Low confidence 220.969 235.572 14.603
    CPEB3 Rooted cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] High confidence 19.9625 35.798 15.8355
    CUL1 Divided Measured cullin homolog 1 (cul-1). [swissprot;acc:q13616] 2353.63 3225.65 1.3705
    FOS Rooted proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 60.8365 77.7233 1.27758
    GOSR2 Measured 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Low confidence 5060.92 5567.34 1.10006
    JUNB Subtracted Ranked transcription factor jun-b. [swissprot;acc:p17275] High confidence 201.144 158.868 42.276
    PPP1R2 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Low confidence 62385.1 53596 8789.1
    PSCD4 Measured cytohesin 4. [swissprot;acc:q9uia0] 12315 11390.6 924.4
    PTPRA Divided Ranked vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] 203.948 189.652 1.07538
    SLC11A2 Rooted natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] 64.1217 69.7 1.087
    SYMPK Subtracted Squared symplekin. [swissprot;acc:q92797] High confidence 124118 88668.8 35449.2
    TRO Divided Ranked trophinin. [swissprot;acc:q12816] 88.2482 110.265 1.24949
    VPS33A Subtracted Rooted vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 69.1897 75.3346 6.1449
    104 no value Divided jun dimerization protein. [refseq;acc:nm_130469] High confidence 60.8365 77.7233 1.27758
    ADIPOR2 Ranked adiponectin receptor 2. [refseq;acc:nm_024551] Low confidence 219.277 204.212 1.07377
    ATP5O Subtracted Squared atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 61860.4 53172.3 8688.1
    CPSF4 Divided 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] 60910.8 52263.5 1.16546
    CSTF2T Subtracted likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] High confidence 121579 87259.3 34319.7
    DGKH Rooted diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence 62.2472 68.3765 6.1293
    HOMER2 Divided Ranked homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 252.371 202.016 1.24926
    MSI2 Measured musashi 2 isoform a. [refseq;acc:nm_138962] 4241.57 5810.79 1.36996
    PANK1 Subtracted pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Low confidence 10665 11587.2 922.2
    PSCD1 Divided Squared cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 407289 263351 1.54656
    RASAL2 Subtracted Rooted ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 19.9625 35.798 15.8355
    RRAGB Divided Measured ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 10618.8 11681.3 1.10006
    SLC11A1 Subtracted Ranked natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] 225.666 211.107 14.559
    STAMBP Measured associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] High confidence 11068 8508.5 2559.5
    TARDBP Ranked tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 256.228 298.438 42.21
    VPS18 Divided Rooted vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 69.2771 75.2308 1.08594
    105 no value Subtracted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] High confidence 63.7477 48.1588 15.5889
    B9D1 Ranked b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Low confidence 213.243 227.616 14.373
    CPSF4 Squared 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] 60910.8 52263.5 8647.3
    DGKD Rooted diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] 62.2472 68.3765 6.1293
    E2F1 Divided Ranked transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] 220.497 205.364 1.07369
    FOSL2 Rooted fos-related antigen 2. [swissprot;acc:p15408] High confidence 60.8675 77.7168 1.27682
    GNB1 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 266.716 333.165 1.24914
    JUND Subtracted transcription factor jun-d. [swissprot;acc:p17535] 200.941 158.941 42
    MSI1 Divided Measured musashi 1. [refseq;acc:nm_002442] 4241.57 5810.79 1.36996
    PPP1R2 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Low confidence 62385.1 53596 1.16399
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 407289 263351 1.54656
    RALGDS Subtracted ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 90432.9 56304.2 34128.7
    RRAGA Divided Measured ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 10585.5 11638.6 1.09949
    SLC16A2 Subtracted monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] 10553.9 11452.8 898.9
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 11068 8508.5 2559.5

    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/