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 green network_comparison
    Results: HTML CSV LaTeX Showing element 223 to 272 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    223 no value pnas-18. [sptrembl;acc:q9bzu3] 12602.7 13939.6 1.10608
    224 CLPX atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 9815.6 8889.93 1.10413
    225 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 11035.3 9997.71 1.10378
    226 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 15395.7 16992.9 1.10374
    227 TIGD6 tigger transposable element derived 6. [refseq;acc:nm_030953] 12360 11200.2 1.10355
    228 SEPSECS soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 10303.5 11370.4
    229 no value poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 10899.4 9878.1 1.10339
    230 TIGD7 tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 12364.7 11207.7 1.10323
    231 TIGD1 tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 12364.8 11207.9 1.10322
    232 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 12394.7 11240.2 1.10271
    233 no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 9586.97 10560 1.1015
    234 transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 16614 18296 1.10124
    235 EEF1AL3 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 14554.5 16027.9 1.10123
    236 PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 15245.4 16788.5 1.10122
    237 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 9984 9067 1.10114
    238 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 12677.7 13941.7 1.0997
    239 MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 8907.41 9795.36 1.09969
    240 no value methyltransferase like 2. [refseq;acc:nm_018396] 17946 16326 1.09923
    241 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 14003.7 12743.3 1.09891
    242 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 15260.6 13895.8 1.09822
    243 PABPC3 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1251 1373 1.09752
    244 KRTAP9-8 keratin associated protein 9.2. [refseq;acc:nm_031961] 10551.1 11579.9 1.09751
    245 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 11867.6 13019 1.09702
    246 no value keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 10551.6 11573.7 1.09687
    247 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
    248 keratin associated protein 1.5. [refseq;acc:nm_031957]
    249 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
    250 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
    251 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 11573.6 1.09686
    252 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 11573.5 1.09685
    253 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
    254 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
    255 STARD6 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
    256 ESPNP espin. [refseq;acc:nm_031475] 11573.4 1.09684
    257 no value keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 10552.2 11566.4 1.09611
    258 40s ribosomal protein s28. [swissprot;acc:p25112] 12967.1 14193.6 1.09459
    259 CAP2 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 10438.3 9549.77 1.09304
    260 RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 12447.6 11392.6 1.0926
    261 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 12448.9 11393.9 1.09259
    262 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 3464 3778 1.09065
    263 NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 13573.3 14801.2 1.09046
    264 no value arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 10037.1 10935.1 1.08947
    265 GYG2 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 13653.8 14874 1.08937
    266 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] 13483.3 14685.4 1.08915
    267 TAF4 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 8054.34 8772.02 1.0891
    268 MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 14257.4 13134.5 1.08549
    269 no value ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 12463.5 11482.6 1.08542
    270 PCYT2 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 10735.1 9891.37 1.0853
    271 no value myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]
    272 sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 7163.55 7759.61 1.08321

    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/