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 280 to 329 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    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
    312 60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L 242.195 266.663 1.10103
    313 ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B 232.473 211.207 1.10069
    314 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] METAP1 244.126 268.604 1.10027
    315 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] METAP2
    316 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] EIF1 242.694 267.017 1.10022
    317 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] no value 224.445 204.044 1.09998
    318 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] MRPL3 242.011 266.18 1.09987
    319 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 240.73 264.729 1.09969
    320 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 241.892 265.96 1.0995
    321 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] no value 265.959 1.09949
    322 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B 86.7483 78.8995 1.09948
    323 60s ribosomal protein l23a. [swissprot;acc:p29316] no value 241.884 265.945 1.09947
    324 40s ribosomal protein s23. [swissprot;acc:p39028] RPS23 243.944 268.195 1.09941
    325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] MRPS12
    326 60s ribosomal protein l5. [swissprot;acc:p46777] RPL5 241.899 265.924 1.09932
    327 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A 243.817 267.962 1.09903
    328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] DDX24 258.437 235.183 1.09888
    329 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 312 284 1.09859

    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/