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 description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2575 to 2624 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    2575 PTPN2 protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] 209.583 1.00157 209.255
    2576 SNTB1 beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 213.422 1.00154 213.75
    2577 CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 192.625 192.922
    2578 SNTB2 beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 213.422 213.75
    2579 NIT1 nitrilase 1. [refseq;acc:nm_005600]
    2580 UTRN utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
    2581 DTNB dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] 213.428 213.756
    2582 DBT lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] 213.422 213.75
    2583 DTNA dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] 213.415 213.743
    2584 no value dystrophin. [swissprot;acc:p11532] 213.422 213.75
    2585 AMOT angiomotin. [refseq;acc:nm_133265]
    2586 AMOTL2 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
    2587 SNTA1 alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]
    2588 HSPD1 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 222.305 1.00151 222.64
    2589 FAM57A membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 212.74 1.0015 212.422
    2590 PSMA6 proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] 214.605 1.00148 214.287
    2591 PBRM1 polybromo 1. [refseq;acc:nm_018165] 220.02 1.00147 219.696
    2592 SMARCA5 swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]
    2593 SMARCA4 possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]
    2594 SMARCA1 possible global transcription activator snf2l1. [swissprot;acc:p28370]
    2595 BTAF1 tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]
    2596 SMARCA2 possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]
    2597 IPO11 ran binding protein 11. [refseq;acc:nm_016338] 212.711 1.00146 212.401
    2598 TAF5 transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] 202.142 1.00145 202.436
    2599 KIAA1432 ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 211.662 1.00142 211.361
    2600 HYAL3 interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] 224.877 1.00141 225.193
    2601 CNNM3 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 214.502 214.2
    2602 ARPC5 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] 224.875 225.192
    2603 CNNM4 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 214.494 214.192
    2604 CNNM2 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] 214.486 214.184
    2605 PRUNE tcd37 homolog; prune. [refseq;acc:nm_021222] 214.495 214.193
    2606 CNNM1 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 214.5 214.198
    2607 MRPS22 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 215.497 1.0014 215.799
    2608 no value nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
    2609 LMX1A lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]
    2610 TOMM70A mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]
    2611 LMX1B lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]
    2612 PSMB2 proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]
    2613 ARL1 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
    2614 RELA transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] 202.821 1.00139 202.54
    2615 RELB transcription factor relb (i-rel). [swissprot;acc:q01201]
    2616 NFKBIA nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
    2617 CPOX coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
    2618 IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] 190.166 1.00138 190.429
    2619 SMARCC2 swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 220.024 1.00137 219.722
    2620 PSMD9 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 215.615 215.91
    2621 no value dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 224.891 1.00135 225.195
    2622 ZMYM6 zinc finger protein 258. [refseq;acc:nm_145310]
    2623 ZMYM3 zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
    2624 ZMYM4 zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]

    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/