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 Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 236 to 285 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    236 pp3111 protein. [refseq;acc:nm_022156] DUS1L 227.357 254.15 1.11785
    237 syntaxin 18. [swissprot;acc:q9p2w9] STX18
    238 rd protein. [swissprot;acc:p18615] no value
    239 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1
    240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1
    241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1
    242 j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12
    243 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13
    244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2
    245 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 226.109 202.333 1.11751
    246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 237.312 212.363 1.11748
    247 rna-binding protein. [refseq;acc:nm_019027] no value 237.302 212.41 1.11719
    248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
    249 ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP
    250 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR
    251 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 186.172 166.661 1.11707
    252 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 237.292 212.457 1.11689
    253 mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 228 204.333 1.11583
    254 source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B 200.691 179.88 1.11569
    255 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A
    256 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 227.999 204.357
    257 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] DDOST 200.691 179.88
    258 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 227.999 204.366 1.11564
    259 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 204.37 1.11562
    260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 219.421 196.978 1.11394
    261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1
    262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1
    263 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2
    264 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] DCPS
    265 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 225.217 202.459 1.11241
    266 transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] SIN3A 241.07 267.88 1.11121
    267 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] DENR
    268 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] EIF5 271.016 244.167 1.10996
    269 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] PCYT1A 241.373 267.352 1.10763
    270 fad synthetase. [refseq;acc:nm_025207] FLAD1
    271 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] no value
    272 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] LGTN
    273 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] PAPSS1
    274 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] POR
    275 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] PCYT1B
    276 60s ribosomal protein l32. [swissprot;acc:p02433] SNORA7A 241.13 266.969 1.10716
    277 40s ribosomal protein s29. [swissprot;acc:p30054] no value 241.849 267.642 1.10665
    278 40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 241.399 267.088 1.10642
    279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] RBBP7 252.644 228.42 1.10605
    280 metastasis-associated protein mta1. [swissprot;acc:q13330] MTA1 252.512 228.356 1.10578
    281 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] no value 241.808 267.335 1.10557
    282 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] RBBP4 252.39 228.297 1.10553
    283 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 241.828 267.346 1.10552
    284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] BCAR1 224.657 203.235 1.10541
    285 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 224.647 203.242 1.10532

    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/