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 green red network_comparison
    Results: HTML CSV LaTeX Showing element 983 to 1032 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		green
    		red
    		network_comparison
    983 RSL1D1 pbk1 protein. [sptrembl;acc:o76021] 235.353 243.312 1.03382
    984 PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 120.654 116.71 1.03379
    985 PDCD5 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 225.782 233.402 1.03375
    986 EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] 120.707 116.771 1.03371
    987 HTRA2 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] 211.338 218.459 1.03369
    988 HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 211.343 218.461 1.03368
    989 HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 211.345 218.462 1.03367
    990 DDX52 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 235.373 243.297
    991 DPM1 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] 196.76 203.381 1.03365
    992 HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 211.357 218.468 1.03364
    993 PNN pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 204.205 211.071 1.03362
    994 PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 120.772 116.845 1.03361
    995 MAD2L2 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 212.547 219.656 1.03345
    996 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
    997 NUP88 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
    998 DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 218.271 225.557 1.03338
    999 VCL vinculin (metavinculin). [swissprot;acc:p18206] 208.95 215.92 1.03336
    1000 no value sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 217.922 225.167 1.03325
    1001 SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
    1002 SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
    1003 SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
    1004 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 231.059 238.725 1.03318
    1005 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 218.232 225.448 1.03307
    1006 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 120.375 116.524 1.03305
    1007 RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 156.884 162.055 1.03296
    1008 WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] 235.475 243.227 1.03292
    1009 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 221.823 229.116 1.03288
    1010 CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 210.648 217.523 1.03264
    1011 RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 210.189 217.026 1.03253
    1012 RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 210.185 217.021 1.03252
    1013 HEATR1 protein bap28. [swissprot;acc:q9h583] 236.647 244.312 1.03239
    1014 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 235.422 243.045 1.03238
    1015 MAGI1 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 228.906 221.73 1.03236
    1016 KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 210.561 217.369 1.03233
    1017 TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 210.558 217.365
    1018 KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 210.554 217.361
    1019 TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 214.409 221.302 1.03215
    1020 DCT dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] 221.28 1.03205
    1021 TYRP1 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] 221.278 1.03204
    1022 CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 199.266 205.632 1.03195
    1023 RHOC transforming protein rhoc (h9). [swissprot;acc:p08134]
    1024 TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
    1025 MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
    1026 RHOA transforming protein rhoa (h12). [swissprot;acc:p06749]
    1027 SUCLG1 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] 218.627 211.908 1.03171
    1028 SUCLA2 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]
    1029 DDB1 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] 215.535 222.364 1.03168
    1030 PCCB 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]
    1031 EMG1 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 235.518 242.978 1.03167
    1032 AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 180.943 186.664 1.03162

    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/