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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 3358 to 3407 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    420 Squared serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Low confidence NEK2 1.06696 42968.8 40272.3
    Rooted dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] High confidence POLE 1.09903 51.7959 56.9253
    [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Low confidence PDK2 1.04743 71.1072 74.4801
    421 Measured latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302] LPHN2 1.05237 8768.68 9227.9
    vav-2 protein. [swissprot;acc:p52735] High confidence VAV2 1.15582 6660.02 7697.78
    Ranked tetraspan net-5. [swissprot;acc:o75954] Low confidence TSPAN9 1.03514 197.897 204.852
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] High confidence TFIP11 1.08403 223.202 205.9
    Squared cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 1.21717 36933 44953.6
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Low confidence no value 1.06695 33447.9 31349.2
    Rooted c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] High confidence 1.09873 50.4666 45.9317
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Low confidence RRAGC 1.0474 79.7288 83.5078
    422 Measured latrophilin 1; lectomedin-2; latrophilin homolog 1 (cow). [refseq;acc:nm_014921] LPHN1 1.05237 8768.68 9227.9
    nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] High confidence NXF5 1.15425 5206.9 6010.04
    Ranked ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 1.08284 240.287 260.193
    zinc finger protein 258. [refseq;acc:nm_145310] Low confidence ZMYM6 1.03512 205.501 198.528
    Squared dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] High confidence MLH3 1.21715 25860 31475.4
    dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Low confidence DKC1 1.0669 47123.2 44168.2
    Rooted 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence RPL5 1.09873 50.4641 45.9293
    methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence MTHFR 1.04734 83.5066 87.4602
    423 Measured nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] High confidence NXF3 1.15423 5207.03 6010.1
    protein tyrosine phosphatase, non-receptor type 14 (ec 3.1.3.48) (protein-tyrosine phosphatase pez). [swissprot;acc:q15678] Low confidence PTPN14 1.0523 8902.76 9368.39
    Ranked ras-related protein rab-26. [swissprot;acc:q9ulw5] High confidence RAB26 1.08284 240.287 260.193
    zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202] Low confidence ZMYM3 1.03512 205.501 198.528
    Squared laminin alpha-5 chain precursor. [swissprot;acc:o15230] LAMA5 1.06684 46091.1 43203.2
    signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] High confidence CBLB 1.21652 36735.7 44689.6
    Rooted epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 1.09873 50.4663 45.9313
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence FBP2 1.04733 74.9331 78.4794
    424 Measured nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] High confidence NXF1 1.15413 5207.78 6010.45
    protein tyrosine phosphatase, non-receptor type 21 (ec 3.1.3.48) (protein-tyrosine phosphatase d1). [swissprot;acc:q16825] Low confidence PTPN21 1.0523 8902.76 9368.39
    Ranked dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] High confidence POLR2C 1.08284 240.287 260.193
    zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095] Low confidence ZMYM4 1.03512 205.501 198.528
    Squared mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] High confidence PMPCA 1.21601 20259.5 24635.7
    ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] Low confidence RPS6KA6 1.06682 48773.8 45718.9
    Rooted 60s ribosomal protein l23a. [swissprot;acc:p29316] High confidence no value 1.09868 50.4703 45.9373
    dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Low confidence SEL1L2 1.04732 74.9096 78.4542
    425 Measured ras-related protein rab-7. [swissprot;acc:p51149] RAB7A 1.05226 8055.75 8476.72
    saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence NIP7 1.15354 3729.02 4301.58
    Ranked max protein. [swissprot;acc:p25912] MAX 1.082 227.828 210.561
    zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Low confidence ZMYM2 1.03512 205.501 198.528
    Squared mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] High confidence PMPCB 1.21601 20258.6 24634.7
    ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Low confidence RPS6KA3 1.06681 48782.8 45727.7
    Rooted 40s ribosomal protein s20. [swissprot;acc:p17075] High confidence RPS20 1.09849 50.0161 45.5318
    sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence SEL1L 1.04732 74.9094 78.454
    426 Measured pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] High confidence PEF1 1.15325 5942.49 6853.15
    proton/amino acid transporter 4. [refseq;acc:nm_152313] Low confidence SLC36A4 1.05223 8913.45 9379.02
    Ranked actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] ACTR3 1.03512 205.501 198.528
    dynactin 4. [refseq;acc:nm_032486] High confidence DCTN5 1.08197 233.142 252.253
    Squared hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Low confidence HGS 1.06677 51199.2 47994.4
    ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] High confidence UQCRC1 1.21596 20267.8 24644.8
    Rooted fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Low confidence FBP1 1.04731 74.8883 78.4313

    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/