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 251 to 300 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		green
    		red
    		network_comparison
    251 SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 166.661 186.172 1.11707
    252 EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 237.292 1.11689
    253 MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 228 1.11583
    254 STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 179.88 200.691 1.11569
    255 STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]
    256 MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 227.999
    257 DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 179.88 200.691
    258 MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 227.999 1.11564
    259 RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 1.11562
    260 HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 219.421 1.11394
    261 HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]
    262 HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
    263 HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
    264 DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]
    265 SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 202.459 225.217 1.11241
    266 SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 267.88 241.07 1.11121
    267 DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
    268 EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 244.167 271.016 1.10996
    269 PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 267.352 241.373 1.10763
    270 FLAD1 fad synthetase. [refseq;acc:nm_025207]
    271 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
    272 LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]
    273 PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]
    274 POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
    275 PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
    276 SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] 266.969 241.13 1.10716
    277 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 267.642 241.849 1.10665
    278 RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] 267.088 241.399 1.10642
    279 RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 228.42 252.644 1.10605
    280 MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] 228.356 252.512 1.10578
    281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 267.335 241.808 1.10557
    282 RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 228.297 252.39 1.10553
    283 RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 267.346 241.828 1.10552
    284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 203.235 224.657 1.10541
    285 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 203.242 224.647 1.10532
    286 NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 203.251 224.633 1.1052
    287 RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 266.079 240.758 1.10517
    288 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078
    289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 246.892 272.781 1.10486
    290 RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 210.064 231.969 1.10428
    291 NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 228.037 251.679 1.10368
    292 RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] 266.414 241.411 1.10357
    293 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 265.717 240.782 1.10356
    294 BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]
    295 SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 202.423 223.273 1.103
    296 MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 266.12 241.282 1.10294
    297 no value 60s ribosomal protein l7. [swissprot;acc:p18124] 259.984 235.727 1.1029
    298 CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 243.588 268.632 1.10281
    299 CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 243.592 268.635
    300 PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 166.351 150.959 1.10196

    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/