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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 262 to 311 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 219.421 196.978 1.11394
    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
    286 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] NEDD9 224.633 203.251 1.1052
    287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] RPS4Y2 240.758 266.079 1.10517
    288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] no value 266.078
    289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486
    290 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 231.969 210.064 1.10428
    291 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] NFYB 251.679 228.037 1.10368
    292 40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A 241.411 266.414 1.10357
    293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] no value 240.782 265.717 1.10356
    294 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] BCCIP
    295 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 223.273 202.423 1.103
    296 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] MRPL4 241.282 266.12 1.10294
    297 60s ribosomal protein l7. [swissprot;acc:p18124] no value 235.727 259.984 1.1029
    298 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] CAPN2 268.632 243.588 1.10281
    299 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 268.635 243.592
    300 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] PITRM1 150.959 166.351 1.10196
    301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 150.982 166.372 1.10193
    302 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 242.326 267.008 1.10185
    303 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 242.333 266.999 1.10179
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value 242.339 266.986 1.1017
    305 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value 242.153 266.673 1.10126
    307 serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR
    308 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34
    309 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2
    310 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1
    311 protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B 242.627 267.151 1.10108

    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/