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 Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1425 to 1474 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    179 Measured f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] FBXW7 Low confidence 1.08076 7004.28 7569.94
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C High confidence 1.29238 21591.5 27904.5
    Ranked 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] RPL6 Low confidence 1.0555 209.954 221.607
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value High confidence 1.16476 226.884 194.79
    Squared homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] HHEX Low confidence 1.11142 64916.3 58408.5
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 High confidence 1.37987 25326.3 18354.1
    Rooted palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] EGFL8 1.15665 50.272 43.4634
    tho complex 3. [refseq;acc:nm_032361] no value Low confidence 1.06314 72.7219 77.3133
    180 Measured myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence 1.29238 21591.5 27904.5
    rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] RHBDL1 Low confidence 1.08076 23239.9 21503.3
    Ranked protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] DCHS1 1.05536 218.925 207.441
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP High confidence 1.16474 256.228 298.438
    Squared plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 1.37987 25326.2 18354.1
    poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] PAPOLG Low confidence 1.11106 51730.2 46559.2
    Rooted egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] EGFL7 High confidence 1.15645 50.2801 43.4779
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 Low confidence 1.06292 63.4976 67.4927
    181 Measured eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 High confidence 1.29102 4068.56 5252.6
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Low confidence 1.08076 7004.28 7569.94
    Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 1.05407 196.362 206.979
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 High confidence 1.16294 229.818 267.265
    Squared hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 1.36766 55630.4 76083.7
    rab9 effector p40. [refseq;acc:nm_005833] RABEPK Low confidence 1.11053 51594.2 46458.9
    Rooted crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] BCAR1 High confidence 1.15472 57.4432 66.3307
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 Low confidence 1.0629 63.5014 67.4959
    182 Measured putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 1.07811 6846.84 6350.78
    rna-binding protein. [refseq;acc:nm_019027] no value High confidence 1.29051 4069.83 5252.17
    Ranked histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 1.15422 277.546 240.461
    px serine/threonine kinase. [refseq;acc:nm_017771] PXK Low confidence 1.05385 196.372 206.947
    Squared 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 1.11042 54678.1 49240.7
    deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] DUT High confidence 1.36506 61733.5 45224.1
    Rooted nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Low confidence 1.06274 69.7469 74.1228
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 High confidence 1.1546 57.45 66.332
    183 Measured apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value 1.29051 4069.83 5252.17
    mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] PBLD Low confidence 1.07763 10087.8 10870.9
    Ranked 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 High confidence 1.153 228.306 198.011
    bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] no value Low confidence 1.05385 196.372 206.947
    Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL High confidence 1.35478 79779.8 108084
    sodium/potassium-transporting atpase beta-1 chain (sodium/potassium- dependent atpase beta-1 subunit). [swissprot;acc:p05026] ATP1B1 Low confidence 1.11042 52767.9 47520.7
    Rooted axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] DNALI1 1.06257 67.0706 71.2671
    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 High confidence 1.15446 57.4586 66.3336
    184 Measured ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP 1.29051 4069.83 5252.17
    spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] no value Low confidence 1.07749 7764.08 8365.72
    Ranked odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 High confidence 1.15239 274.027 237.79
    testis specific, 10. [refseq;acc:nm_025244] TSGA10 Low confidence 1.05384 196.373 206.946
    Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] no value High confidence 1.35203 72886.3 98544.5
    spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] SRM Low confidence 1.11039 54936 49474.7
    Rooted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A High confidence 1.15321 153.602 133.195
    u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] SNRPB2 Low confidence 1.06257 70.6712 75.0934
    185 Measured heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR High confidence 1.29051 4069.83 5252.17
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] no value Low confidence 1.07736 6852.7 6360.64

    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/