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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 982 to 1031 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    982 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] CIRH1A 243.312 235.351 1.03383
    983 pbk1 protein. [sptrembl;acc:o76021] RSL1D1 235.353 1.03382
    984 poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] PAPOLA 116.71 120.654 1.03379
    985 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] PDCD5 233.402 225.782 1.03375
    986 exocyst complex component sec5. [swissprot;acc:q96kp1] EXOC2 116.771 120.707 1.03371
    987 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] HTRA2 218.459 211.338 1.03369
    988 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] HTRA4 218.461 211.343 1.03368
    989 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] HTRA3 218.462 211.345 1.03367
    990 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] DDX52 243.297 235.373
    991 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] DPM1 203.381 196.76 1.03365
    992 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] HTRA1 218.468 211.357 1.03364
    993 pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] PNN 211.071 204.205 1.03362
    994 poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] PAPOLG 116.845 120.772 1.03361
    995 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] MAD2L2 219.656 212.547 1.03345
    996 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] no value
    997 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] NUP88
    998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] DYNC1I2 225.557 218.271 1.03338
    999 vinculin (metavinculin). [swissprot;acc:p18206] VCL 215.92 208.95 1.03336
    1000 sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] no value 225.167 217.922 1.03325
    1001 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] SPRY3
    1002 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] SPRY1
    1003 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] SPRY2
    1004 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] no value 238.725 231.059 1.03318
    1005 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] DYNC1I1 225.448 218.232 1.03307
    1006 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] CPSF3 116.524 120.375 1.03305
    1007 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] RALGDS 162.055 156.884 1.03296
    1008 wd-repeat protein bing4. [swissprot;acc:o15213] WDR46 243.227 235.475 1.03292
    1009 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] no value 229.116 221.823 1.03288
    1010 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] CROT 217.523 210.648 1.03264
    1011 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] RBL2 217.026 210.189 1.03253
    1012 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] RBL1 217.021 210.185 1.03252
    1013 protein bap28. [swissprot;acc:q9h583] HEATR1 244.312 236.647 1.03239
    1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] AATF 243.045 235.422 1.03238
    1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] MAGI1 221.73 228.906 1.03236
    1016 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] KPNA4 217.369 210.561 1.03233
    1017 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] TOE1 217.365 210.558
    1018 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] KPNA3 217.361 210.554
    1019 tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] TYRL 221.302 214.409 1.03215
    1020 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] DCT 221.28 1.03205
    1021 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] TYRP1 221.278 1.03204
    1022 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS 205.632 199.266 1.03195
    1023 transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC
    1024 thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST
    1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST
    1026 transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA
    1027 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] SUCLG1 211.908 218.627 1.03171
    1028 succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] SUCLA2
    1029 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] DDB1 222.364 215.535 1.03168
    1030 propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] PCCB
    1031 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] EMG1 242.978 235.518 1.03167

    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/