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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1986 to 2035 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    993 PNN pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] High confidence 211.071 204.205 1.03362
    994 OGDH 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] Low confidence 201.562 196.729 1.02457
    PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] High confidence 116.845 120.772 1.03361
    995 MAD2L2 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 219.656 212.547 1.03345
    USP2 ubiquitin carboxyl-terminal hydrolase 2 (ec 3.1.2.15) (ubiquitin thiolesterase 2) (ubiquitin-specific processing protease 2) (deubiquitinating enzyme 2) (41 kda ubiquitin-specific protease). [swissprot;acc:o75604] Low confidence 200.373 195.574 1.02454
    996 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 219.656 212.547 1.03345
    PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Low confidence 204.965 200.057 1.02453
    997 no value rd protein. [swissprot;acc:p18615]
    NUP88 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] High confidence 219.656 212.547 1.03345
    998 DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 225.557 218.271 1.03338
    WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Low confidence 199.985 195.196 1.02453
    999 DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] 204.965 200.057
    VCL vinculin (metavinculin). [swissprot;acc:p18206] High confidence 215.92 208.95 1.03336
    1000 no value sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 225.167 217.922 1.03325
    HCLS1 hematopoietic lineage cell specific protein (hematopoietic cell- specific lyn substrate 1) (lckbp1). [swissprot;acc:p14317] Low confidence 199.945 195.159 1.02452
    1001 CASKIN1 rna-binding protein s1, serine-rich domain; sr protein. [refseq;acc:nm_006711] 206.276 201.339
    SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] High confidence 225.167 217.922 1.03325
    1002 BRD7 bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] Low confidence 205.137 200.227 1.02452
    SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] High confidence 225.167 217.922 1.03325
    1003 NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] Low confidence 191.663 187.077 1.02451
    SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] High confidence 225.167 217.922 1.03325
    1004 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 231.059 1.03318
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Low confidence 200.403 195.612 1.02449
    1005 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] High confidence 225.448 218.232 1.03307
    USP5 ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974] Low confidence 204.271 199.392 1.02447
    1006 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] High confidence 116.524 120.375 1.03305
    GIT1 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] Low confidence 206.183 201.259 1.02447
    1007 ETFDH electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] 198.075 193.349 1.02444
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] High confidence 162.055 156.884 1.03296
    1008 CTTN src substrate cortactin (amplaxin) (oncogene ems1). [swissprot;acc:q14247] Low confidence 199.992 195.221 1.02444
    WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] High confidence 243.227 235.475 1.03292
    1009 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 229.116 221.823 1.03288
    PDZD4 lu1 protein. [refseq;acc:nm_032512] Low confidence 204.391 199.514 1.02444
    1010 BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 202.366 197.54 1.02443
    CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] High confidence 217.523 210.648 1.03264
    1011 LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Low confidence 208.97 214.075 1.02443
    RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] High confidence 217.026 210.189 1.03253
    1012 RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 217.021 210.185 1.03252
    SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Low confidence 204.877 199.992 1.02443
    1013 HEATR1 protein bap28. [swissprot;acc:q9h583] High confidence 244.312 236.647 1.03239
    IMPDH2 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Low confidence 200.743 195.959 1.02441
    1014 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] High confidence 243.045 235.422 1.03238
    MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence 182.56 178.211 1.0244
    1015 KIFC3 kinesin family member c3. [refseq;acc:nm_005550] 205.25 200.362
    MAGI1 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] High confidence 221.73 228.906 1.03236
    1016 KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 217.369 210.561 1.03233
    TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Low confidence 201.283 196.49 1.02439
    1017 IMPDH1 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] 200.745 195.966
    TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] High confidence 217.365 210.558 1.03233
    1018 KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 210.554

    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/