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 Rank Value Type Hugo Network Comparison Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1630 to 1679 of 66312 in total
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    102 Rooted DGKQ Divided diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Low confidence 1.08856 61.2565 66.6812
    DVL2 Subtracted segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 6.1843 68.5063 74.6906
    RAP1GAP Divided rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] High confidence 1.29028 47.6504 36.9304
    103 Measured CHMP2A Subtracted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 2559.5 11068 8508.5
    CUL1 Divided cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1.3705 2353.63 3225.65
    GOSR2 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Low confidence 1.10006 5060.92 5567.34
    PSCD4 Subtracted cytohesin 4. [swissprot;acc:q9uia0] 924.4 12315 11390.6
    Ranked COL4A3BP 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] 14.603 220.969 235.572
    JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 42.276 201.144 158.868
    PTPRA Divided vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence 1.07538 203.948 189.652
    TRO trophinin. [swissprot;acc:q12816] High confidence 1.24949 88.2482 110.265
    Squared no value 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] 1.54656 407289 263351
    BNC1 zinc finger protein basonuclin. [swissprot;acc:q01954] Low confidence 1.16733 105225 90141.3
    PPP1R2 Subtracted protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 8789.1 62385.1 53596
    SYMPK symplekin. [swissprot;acc:q92797] High confidence 35449.2 124118 88668.8
    Rooted CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 15.8355 19.9625 35.798
    FOS Divided proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 1.27758 60.8365 77.7233
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 1.087 64.1217 69.7
    VPS33A Subtracted vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] 6.1449 69.1897 75.3346
    104 Measured MSI2 Divided musashi 2 isoform a. [refseq;acc:nm_138962] High confidence 1.36996 4241.57 5810.79
    PANK1 Subtracted pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Low confidence 922.2 10665 11587.2
    RRAGB Divided ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 1.10006 10618.8 11681.3
    STAMBP Subtracted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] High confidence 2559.5 11068 8508.5
    Ranked ADIPOR2 Divided adiponectin receptor 2. [refseq;acc:nm_024551] Low confidence 1.07377 219.277 204.212
    HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 1.24926 252.371 202.016
    SLC11A1 Subtracted natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 14.559 225.666 211.107
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] High confidence 42.21 256.228 298.438
    Squared ATP5O atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Low confidence 8688.1 61860.4 53172.3
    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] 1.16546 60910.8 52263.5
    CSTF2T Subtracted likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] High confidence 34319.7 121579 87259.3
    PSCD1 Divided cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1.54656 407289 263351
    Rooted no value jun dimerization protein. [refseq;acc:nm_130469] 1.27758 60.8365 77.7233
    DGKH Subtracted diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence 6.1293 62.2472 68.3765
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] High confidence 15.8355 19.9625 35.798
    VPS18 Divided vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 1.08594 69.2771 75.2308
    105 Measured MSI1 musashi 1. [refseq;acc:nm_002442] High confidence 1.36996 4241.57 5810.79
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 1.09949 10585.5 11638.6
    SLC16A2 Subtracted monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] 898.9 10553.9 11452.8
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 2559.5 11068 8508.5
    Ranked B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Low confidence 14.373 213.243 227.616
    E2F1 Divided 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] 1.07369 220.497 205.364
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] High confidence 1.24914 266.716 333.165
    JUND Subtracted transcription factor jun-d. [swissprot;acc:p17535] 42 200.941 158.941
    Squared CPSF4 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] Low confidence 8647.3 60910.8 52263.5
    PPP1R2 Divided protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 1.16399 62385.1 53596
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 1.54656 407289 263351
    RALGDS Subtracted ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 34128.7 90432.9 56304.2
    Rooted no value 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] 15.5889 63.7477 48.1588
    DGKD diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence 6.1293 62.2472 68.3765
    FOSL2 Divided fos-related antigen 2. [swissprot;acc:p15408] High confidence 1.27682 60.8675 77.7168

    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/