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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3051 to 3100 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670] 2729 OTUB1 202.123 202.06 1.00031
    ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] 2681 OTUB2 203.592 203.787 1.00096
    ubiquitin. [swissprot;acc:p02248] 1148 no value 209.061 203.518 1.02724
    1190 UBB 209.6 204.372 1.02558
    2310 UBC 216.617 215.529 1.00505
    ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] 2333 TMOD3 229.258 230.294 1.00452
    udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] 2810 UGT2A1 0.00001 0.00001 1
    udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 1338 GALE 215.162 210.412 1.02257
    udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] 2299 UGDH 215.239 216.339 1.00511
    udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224] 2835 UGT1A9 0.00001 0.00001 1
    udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 3085 UGT2B10
    udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 2819 no value
    udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 3086
    udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 2793
    udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [swissprot;acc:q9by64] 2979 UGT2B28
    udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 2889 UGT2B4
    udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662] 2818 UGT2B7
    udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] 1265 DPAGT1 171.231 167.177 1.02425
    udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] 2401 OGT 182.4 183.083 1.00374
    ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 345 CMPK 242.14 265.697 1.09729
    unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] 2522 UNC119 215.835 216.341 1.00234
    uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 3030 C6orf35 0.00001 0.00001 1
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 29 PPP2R2D 187.458 243.678 1.29991
    unr protein. [swissprot;acc:o75534] 828 CSDE1 230.087 220.579 1.0431
    upf0183 protein. [swissprot;acc:q9bsu1] 2417 C16orf70 218.2 218.984 1.00359
    upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 760 NAT10 246.055 234.458 1.04946
    upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 1191 UBP1 220.742 215.237 1.02558
    upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] 1358 USF1 214.987 210.359 1.022
    upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] 1361 USF2 214.971 210.354 1.02195
    uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 1220 UNG 211.959 217.258 1.025
    uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] 755 UMPS 224.434 235.583 1.04968
    uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533] 2772 NUDT14 0.00001 0.00001 1
    uridine kinase-like 1. [swissprot;acc:q9nwz5] 1502 no value 218.084 214.149 1.01838
    uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132] 3010 UROD 0.00001 0.00001 1
    utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 1609 UGP2 208.113 204.876 1.0158
    utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] 2580 UTRN 213.422 213.75 1.00154
    uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] 1431 RAD23A 220.987 225.468 1.02028
    uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] 1434 RAD23B
    uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] 1311 UXT 226.439 221.26 1.02341
    vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384] 3136 VRK1 0.00001 0.00001 1
    vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296] 3204 VRK2
    vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 1175 ATP6V0C 218.186 212.672 1.02593
    vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] 1180 ATP6V0B
    vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] 1056 ATP6V1A 219.01 212.468 1.03079
    vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787] 2782 ATP6AP2 0.00001 0.00001 1
    vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 1135 ATP6V1B2 218.484 212.675 1.02731
    vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] 1146 ATP6V1B1 218.483 212.676 1.0273
    vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] 1142 ATP6V1D 218.484 212.675 1.02731
    vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] 1187 ATP6V0D1 218.402 212.904 1.02582
    vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] 1138 ATP6V1E1 218.484 212.675 1.02731

    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/