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 [...,...].
    Gene Rank Hugo description Network Comparison Type Value Type Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 973 to 1022 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		network_comparison
    		red
    		green
    973 TULP3 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 1.03426 211.987 204.964
    974 VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
    975 PRKCZ protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
    976 WDR36 t-cell activation wd repeat protein. [refseq;acc:nm_139281] 1.03407 243.34 235.322
    977 PFDN5 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 1.03402 228.953 221.421
    978 no value prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
    979 BLOC1S1 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 1.03399 202.027 195.386
    980 BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 1.03396 130.289 134.713
    981 EXOC3 exocyst complex component sec6. [swissprot;acc:o60645] 1.03387 207.186 200.398
    982 CIRH1A cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 1.03383 243.312 235.351
    983 RSL1D1 pbk1 protein. [sptrembl;acc:o76021] 1.03382 235.353
    984 PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 1.03379 116.71 120.654
    985 PDCD5 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 1.03375 233.402 225.782
    986 EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] 1.03371 116.771 120.707
    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] 1.03369 218.459 211.338
    988 HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 1.03368 218.461 211.343
    989 HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 1.03367 218.462 211.345
    990 DDX52 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 243.297 235.373
    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] 1.03365 203.381 196.76
    992 HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 1.03364 218.468 211.357
    993 PNN pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 1.03362 211.071 204.205
    994 PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 1.03361 116.845 120.772
    995 MAD2L2 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 1.03345 219.656 212.547
    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] 1.03338 225.557 218.271
    999 VCL vinculin (metavinculin). [swissprot;acc:p18206] 1.03336 215.92 208.95
    1000 no value sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 1.03325 225.167 217.922
    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] 1.03318 238.725 231.059
    1005 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 1.03307 225.448 218.232
    1006 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 1.03305 116.524 120.375
    1007 RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 1.03296 162.055 156.884
    1008 WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] 1.03292 243.227 235.475
    1009 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 1.03288 229.116 221.823
    1010 CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 1.03264 217.523 210.648
    1011 RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 1.03253 217.026 210.189
    1012 RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 1.03252 217.021 210.185
    1013 HEATR1 protein bap28. [swissprot;acc:q9h583] 1.03239 244.312 236.647
    1014 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 1.03238 243.045 235.422
    1015 MAGI1 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 1.03236 221.73 228.906
    1016 KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 1.03233 217.369 210.561
    1017 TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 217.365 210.558
    1018 KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 210.554
    1019 TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 1.03215 221.302 214.409
    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] 1.03205 221.28
    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] 1.03204 221.278
    1022 CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 1.03195 205.632 199.266

    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/