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 2808 to 2857 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    702 SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Measured 7067.46 7909.27 1.11911
    703 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 6912.56 7735.12 1.11899
    KIAA0430 limkain b1. [refseq;acc:nm_019081] Ranked 220.438 209.118 1.05413
    POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Rooted 51.4945 48.0189 1.07238
    SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Squared 25114 29386 1.1701
    704 no value alpha-nac protein. [sptrembl;acc:q9h009] Measured 6912.27 7734.68 1.11898
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Ranked 220.438 209.118 1.05413
    ACBD3 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Squared 25114 29386 1.1701
    STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 57.2102 53.3508 1.07234
    705 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Ranked 220.438 209.118 1.05413
    DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Measured 6912.09 7734.41 1.11897
    SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Squared 25114 29386 1.1701
    STX6 syntaxin 6. [swissprot;acc:o43752] Rooted 57.2202 53.3639 1.07226
    706 DIRAS2 di-ras2. [refseq;acc:nm_017594] Measured 6912.08 7734.39 1.11897
    DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Ranked 220.438 209.118 1.05413
    MARCH8 cellular modulator of immune recognition. [refseq;acc:nm_145021] Squared 25114 29386 1.1701
    SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Rooted 60.6572 64.9858 1.07136
    707 ATP6V0B vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Squared 25114 29386 1.1701
    KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Ranked 220.438 209.118 1.05413
    RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Measured 5317.78 5944.25 1.11781
    TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Rooted 74.8348 80.1352 1.07083
    708 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked 220.438 209.118 1.05413
    PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Rooted 74.8348 80.1352 1.07083
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Measured 5317.78 5944.25 1.11781
    TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Squared 19970 23366.8 1.1701
    709 FTL ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Ranked 220.438 209.118 1.05413
    SGCG gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Squared 25114 29386 1.1701
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted 80.4069 86.1018 1.07083
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Measured 5317.78 5944.25 1.11781
    710 DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Ranked 220.438 209.118 1.05413
    FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Measured 5317.78 5944.25 1.11781
    RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Squared 51519.3 44060.4 1.16929
    SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Rooted 69.2869 74.1856 1.0707
    711 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Measured 5317.78 5944.25 1.11781
    COQ3 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Squared 25626.4 29950.3 1.16873
    DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Rooted 58.3914 62.5196 1.0707
    YARS tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Ranked 232.468 245.048 1.05411
    712 ATP5S atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Squared 25626.4 29950.3 1.16873
    FTHL17 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Ranked 220.431 209.123 1.05407
    SREBF1 sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Measured 5317.78 5944.25 1.11781
    VCL vinculin (metavinculin). [swissprot;acc:p18206] Rooted 62.9163 67.3603 1.07063
    713 EIF3M dendritic cell protein. [refseq;acc:nm_006360] Ranked 223.121 211.685 1.05402
    GDA guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Squared 25626.4 29950.3 1.16873
    NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Measured 3996.81 4465.61 1.11729
    SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Rooted 69.3627 74.2575 1.07057
    714 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Measured 5222.71 5834.57 1.11715
    histone deacetylase 2 (hd2). [swissprot;acc:q92769] Rooted 61.0082 65.306 1.07045
    ATP6V1F vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Squared 25904.2 30273.7 1.16868
    CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Ranked 223.121 211.685 1.05402
    715 no value vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Squared 25911.5 30281.9 1.16867

    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/