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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1130 to 1179 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    283 KLF5 Rooted krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] 57.9819 64.9302 1.11984
    POLI Measured polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1.20935
    RPL11 Ranked 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
    284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 203.235 1.10541
    CLEC3A Squared c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 59464 76120.8 1.28012
    CSRP1 Rooted cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 51.8647 46.3161 1.1198
    PXN Measured paxillin. [swissprot;acc:p49023] 5221.28 6314.35 1.20935
    285 CCT4 Ranked t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 224.647 203.242 1.10532
    DDX54 Rooted atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 48.4278 54.2262 1.11973
    DTX1 Squared deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 6680.89 8549.44 1.27969
    PAPOLA Measured poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 23326.5 19296.4 1.20885
    286 CSRP2 Rooted smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 51.8717 46.3287 1.11965
    EXOC2 Measured exocyst complex component sec5. [swissprot;acc:q96kp1] 23316 19288.8 1.20878
    NEDD9 Ranked 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] 224.633 203.251 1.1052
    PBK Squared t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 6693.64 8564.94 1.27956
    287 KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
    PAPOLG Measured poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 23303.1 19279.5 1.2087
    RPS4Y2 Ranked 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 266.079 1.10517
    SHCBP1 Rooted likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 51.8714 46.3281 1.11965
    288 no value Ranked 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 266.078 1.10517
    CPSF3 Measured cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 23422.4 19380.3 1.20857
    CSRP3 Rooted lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 51.8789 46.3416 1.11949
    KHDRBS1 Squared kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 6693.64 8564.94 1.27956
    289 no value Ranked hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486
    KHDRBS2 Squared kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 6693.64 8564.94 1.27956
    LSM6 Measured u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 4682.88 5646.19 1.20571
    PRPF31 Rooted pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 57.4274 64.2609 1.11899
    290 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 1.11788
    NCBP2 Squared 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 15734.4 20126.8 1.27916
    RRM2 Ranked ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 231.969 210.064 1.10428
    TFIP11 Measured tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 4991.48 6014.08 1.20487
    291 no value Rooted ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 113.983 101.979 1.11771
    CLEC3B Squared tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 59016.1 75486.9 1.27909
    NFYB Ranked 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] 251.679 228.037 1.10368
    UBAC1 Measured putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 36927.5 1.20481
    292 LSM6 Rooted u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 56.48 63.119 1.11755
    NEURL Squared neuralized-like. [refseq;acc:nm_004210] 6828.26 8728.66 1.27831
    NUBP1 Measured nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 4641.09 5588.75 1.20419
    RPS15A Ranked 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 266.414 1.10357
    293 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 265.717 1.10356
    KYNU Squared kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 35991.8 46002.9 1.27815
    NUBP2 Measured nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 4641.09 5588.75 1.20419
    TRPC4 Rooted short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 63.0715 56.4506 1.11729
    294 AGPAT2 Squared 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 30826.5 39383.9 1.2776
    BCCIP Ranked 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] 240.782 265.717 1.10356
    CSTF3 Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 22515.5 18702.6 1.20387
    DVL1 Rooted segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 59.0296 65.951 1.11725
    295 no value Squared 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 30807.7 39351.7 1.27733
    DVL2 Rooted segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 59.029 65.9421 1.11711
    RGL1 Measured ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 13261.9 11017.8 1.20368

    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/