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 1651 to 1700 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    826 CTSB cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Low confidence 201.026 195.916 1.02608
    HTATIP 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] High confidence 223.186 213.912 1.04335
    827 LOH12CR1 loh1cr12. [refseq;acc:nm_058169] 230.087 220.579 1.0431
    SPTLC1 serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Low confidence 207.116 201.851 1.02608
    828 COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 204.206 199.02 1.02606
    CSDE1 unr protein. [swissprot;acc:o75534] High confidence 230.087 220.579 1.0431
    829 PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Low confidence 202.608 197.472 1.02601
    SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] High confidence 135.844 130.259 1.04288
    830 FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Low confidence 201.067 195.971 1.026
    PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] High confidence 231.734 222.222 1.0428
    831 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
    TMLHE trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Low confidence 204.064 198.895 1.02599
    832 no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] High confidence 231.734 222.222 1.0428
    GABBR2 gamma-aminobutyric acid type b receptor, subunit 2 precursor (gaba-b receptor 2) (gaba-b-r2) (gb2) (gababr2) (g protein-coupled receptor 51) (gpr 51) (hg20). [swissprot;acc:o75899] Low confidence 204.064 198.895 1.02599
    833 ERAL1 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
    PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] High confidence 231.734 222.222 1.0428
    834 RPL8 60s ribosomal protein l8. [swissprot;acc:p25120]
    TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Low confidence 206.26 201.038 1.02598
    835 HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] High confidence 231.734 222.222 1.0428
    PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Low confidence 202.578 197.45 1.02597
    836 HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] High confidence 231.734 222.222 1.0428
    RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Low confidence 202.357 197.234 1.02597
    837 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 194.47 189.552 1.02595
    DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] High confidence 231.734 222.222 1.0428
    838 GLO1 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Low confidence 194.47 189.552 1.02595
    TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] High confidence 231.734 222.222 1.0428
    839 CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 177.776 170.499 1.04268
    LYPLA1 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Low confidence 194.47 189.552 1.02595
    840 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 201.924 196.817
    TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] High confidence 198.781 190.66 1.04259
    841 PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
    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] Low confidence 206.243 201.027 1.02595
    842 CCDC22 jm1 protein. [refseq;acc:nm_014008] High confidence 219.762 210.806 1.04248
    DCT dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Low confidence 206.244 201.028 1.02595
    843 GART trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] High confidence 218.521 227.796 1.04244
    LYPLA2P1 lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Low confidence 194.47 189.552 1.02595
    844 API5 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 194.659 189.74 1.02592
    CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] High confidence 178.033 170.82 1.04223
    845 ALDH3B2 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Low confidence 209.59 215.023 1.02592
    LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] High confidence 228.599 219.399 1.04193
    846 no value methyltransferase like 2. [refseq;acc:nm_018396] 147.211 153.371 1.04184
    FOXO1 forkhead box protein o1a (forkhead in rhabdomyosarcoma). [swissprot;acc:q12778] Low confidence 204.497 199.336 1.02589
    847 DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] High confidence 147.211 153.371 1.04184
    MLH3 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Low confidence 203.643 198.505 1.02588
    848 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] High confidence 147.211 153.371 1.04184
    SLC16A2 monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Low confidence 181.638 177.058 1.02587
    849 PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] High confidence 147.211 153.371 1.04184
    SLC16A10 solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Low confidence 181.639 177.059 1.02587
    850 CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] High confidence 107.842 112.329 1.04161
    UBL4A ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Low confidence 197.337 192.361 1.02587

    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/