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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2580 to 2629 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2580 utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] UTRN 213.422 213.75 1.00154
    2581 dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] DTNB 213.428 213.756
    2582 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] DBT 213.422 213.75
    2583 dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] DTNA 213.415 213.743
    2584 dystrophin. [swissprot;acc:p11532] no value 213.422 213.75
    2585 angiomotin. [refseq;acc:nm_133265] AMOT
    2586 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] AMOTL2
    2587 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] SNTA1
    2588 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] HSPD1 222.305 222.64 1.00151
    2589 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] FAM57A 212.74 212.422 1.0015
    2590 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] PSMA6 214.605 214.287 1.00148
    2591 polybromo 1. [refseq;acc:nm_018165] PBRM1 220.02 219.696 1.00147
    2592 swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] SMARCA5
    2593 possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] SMARCA4
    2594 possible global transcription activator snf2l1. [swissprot;acc:p28370] SMARCA1
    2595 tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] BTAF1
    2596 possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] SMARCA2
    2597 ran binding protein 11. [refseq;acc:nm_016338] IPO11 212.711 212.401 1.00146
    2598 transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] TAF5 202.142 202.436 1.00145
    2599 ba207c16.2 (fragment). [sptrembl;acc:q9nql7] KIAA1432 211.662 211.361 1.00142
    2600 interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] HYAL3 224.877 225.193 1.00141
    2601 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] CNNM3 214.502 214.2
    2602 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] ARPC5 224.875 225.192
    2603 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] CNNM4 214.494 214.192
    2604 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] CNNM2 214.486 214.184
    2605 tcd37 homolog; prune. [refseq;acc:nm_021222] PRUNE 214.495 214.193
    2606 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] CNNM1 214.5 214.198
    2607 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] MRPS22 215.497 215.799 1.0014
    2608 nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] no value
    2609 lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] LMX1A
    2610 mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] TOMM70A
    2611 lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] LMX1B
    2612 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] PSMB2
    2613 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] ARL1
    2614 transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] RELA 202.821 202.54 1.00139
    2615 transcription factor relb (i-rel). [swissprot;acc:q01201] RELB
    2616 nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963] NFKBIA
    2617 coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551] CPOX
    2618 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] IDH2 190.166 190.429 1.00138
    2619 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] SMARCC2 220.024 219.722 1.00137
    2620 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] PSMD9 215.615 215.91
    2621 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] no value 224.891 225.195 1.00135
    2622 zinc finger protein 258. [refseq;acc:nm_145310] ZMYM6
    2623 zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202] ZMYM3
    2624 zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095] ZMYM4
    2625 wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] WTAP 204.304 204.028
    2626 actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142] ACTR2 224.891 225.195
    2627 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] COG3
    2628 similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] ACTR3B
    2629 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] ARPC1B

    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/