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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 6436 to 6485 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    3218 UGDH udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Low confidence 200.841 197.682 1.01598
    3219 TES testin (tess). [swissprot;acc:q9ugi8] 200.581 197.428 1.01597
    VTA1 protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] High confidence 0.00001 0.00001 1
    3220 no value 60s ribosomal protein l39. [swissprot;acc:p02404] Low confidence 202.665 199.481 1.01596
    TFAP2B transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] High confidence 0.00001 0.00001 1
    3221 HCCS cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Low confidence 200.125 196.981 1.01596
    PAFAH1B1 platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034] High confidence 0.00001 0.00001 1
    3222 no value serine/threonine kinase 38 like. [refseq;acc:nm_015000] Low confidence 200.25 197.107 1.01595
    ALDH3B1 aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] High confidence 0.00001 0.00001 1
    3223 KLHL1 kelch-like protein 1. [swissprot;acc:q9nr64] Low confidence 204.526 201.316 1.01595
    RALA ras-related protein ral-a. [swissprot;acc:p11233] High confidence 0.00001 0.00001 1
    3224 ITGA3 integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006]
    SMAP1 stromal membrane-associated protein; stromal membrane-associated protein smap1a. [refseq;acc:nm_021940] Low confidence 202.662 199.481 1.01595
    3225 HSPB6 heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] High confidence 0.00001 0.00001 1
    STK38 serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271] Low confidence 200.247 197.104 1.01595
    3226 no value ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] High confidence 0.00001 0.00001 1
    KLHL5 kelch-like protein 5. [swissprot;acc:q96pq7] Low confidence 204.526 201.316 1.01595
    3227 ICA1 69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084] High confidence 0.00001 0.00001 1
    KLHL4 kelch-like protein 4. [swissprot;acc:q9c0h6] Low confidence 204.526 201.316 1.01595
    3228 no value alpha-n-acetylgalactosaminidase precursor (ec 3.2.1.49) (alpha- galactosidase b). [swissprot;acc:p17050]
    SCYL3 ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423] High confidence 0.00001 0.00001 1
    3229 COX6B1 cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854] Low confidence 201.768 198.603 1.01594
    3230 UROD uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132]
    3231 HDAC11 histone deacetylase 11 (hd11). [swissprot;acc:q96db2] 203.497 200.309 1.01592
    3232 FEZ1 fasciculation and elongation protein zeta 1 (zygin i). [swissprot;acc:q99689] 201.325 198.17
    3233 REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 198.933 195.816
    3234 TCP11 t-complex 11. [refseq;acc:nm_018679] 199.899 196.766
    3235 COPS5 cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] 203.497 200.309
    3236 WDFY2 wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] 201.246 198.095 1.01591
    3237 CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 199.985 196.854
    3238 PNO1 putatative 28 kda protein. [refseq;acc:nm_020143] 203.258 200.076 1.0159
    3239 FEZ2 fasciculation and elongation protein zeta 2 (zygin ii). [swissprot;acc:q9uhy8] 201.337 198.187 1.01589
    3240 PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 194.562 191.518
    3241 GATAD1 ocular development-associated gene. [refseq;acc:nm_021167] 201.945 198.789 1.01588
    3242 NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] 200.654 203.841
    3243 WDFY1 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] 201.242 198.097
    3244 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] 202.556 199.391 1.01587
    3245 SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 201.31 198.167 1.01586
    3246 NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]
    3247 HNRPH3 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 202.663 199.5 1.01585
    3248 WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 191.496 188.51 1.01584
    3249 no value potential phospholipid-transporting atpase vc (ec 3.6.3.1) (atpvc) (aminophospholipid translocase vc). [swissprot;acc:o60312] 201.185 198.048
    3250 SPEN smart/hdac1 associated repressor protein; msx2 interacting nuclear target (mint) homolog. [refseq;acc:nm_015001] 205.24 202.04
    3251 PPID 40 kda peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin-40) (cyp-40) (cyclophilin-related protein). [swissprot;acc:q08752] 197.955 194.871 1.01583
    3252 CDA cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 200.267 197.148 1.01582
    3253 B3GNT1 n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] 202.38 199.231 1.01581
    3254 HNRPH1 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 202.677 199.525 1.0158
    3255 UBE2G2 ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] 202.137 198.997 1.01578
    3256 EPHX1 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 200.756 197.638
    3257 POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 202.172 199.032

    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/