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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2230 to 2279 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    279 Subtracted AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Squared 30596.2 38919.9 8323.7
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Rooted 42.0574 50.4237 8.3663
    PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked 242.66 265.715 23.055
    280 Divided no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Rooted 57.9068 64.8562 1.12001
    MSI1 musashi 1. [refseq;acc:nm_002442] Squared 15569.5 19953.6 1.28158
    MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked 252.512 228.356 1.10578
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Measured 3119.98 2579.49 1.20953
    Subtracted AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Squared 30566.4 38866.5 8300.1
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted 42.0577 50.424 8.3663
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured 677.5 1865.5 1188
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 267.208 244.168 23.04
    281 Divided no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Measured 3119.98 2579.49 1.20953
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Rooted 57.9068 64.8562 1.12001
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Squared 15569.5 19953.6 1.28158
    Subtracted DYNLT3 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 52623.3 44380.3 8243
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Rooted 42.0684 50.4323 8.3639
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 677.5 1865.5 1188
    MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Ranked 242.159 265.104 22.945
    282 Divided CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Squared 59704 76460.4 1.28066
    RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Measured 3119.98 2579.49 1.20953
    RBBP4 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] Ranked 252.39 228.297 1.10553
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted 57.9819 64.9302 1.11984
    Subtracted KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 108.671 100.365 8.306
    MRE11A double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Squared 52623.3 44380.3 8243
    NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 22.945
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 677.5 1865.5 1188
    283 Divided DTX2 deltex 2. [refseq;acc:nm_020892] Squared 6627.24 8484.19 1.2802
    KLF5 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] Rooted 57.9819 64.9302 1.11984
    POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Measured 5221.28 6314.35 1.20935
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked 241.828 267.346 1.10552
    Subtracted CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared 36933 44953.6 8020.6
    FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Measured 677.5 1865.5 1188
    MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Ranked 242.37 265.255 22.885
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted 108.659 100.356 8.303
    284 Divided BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Ranked 224.657 203.235 1.10541
    CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 1.28012
    CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Rooted 51.8647 46.3161 1.1198
    PXN paxillin. [swissprot;acc:p49023] Measured 5221.28 6314.35 1.20935
    Subtracted no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 677.5 1865.5 1188
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Rooted 108.659 100.356 8.303
    CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Squared 36735.7 44689.6 7953.9
    POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked 242.686 265.516 22.83
    285 Divided CCT4 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 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Rooted 48.4278 54.2262 1.11973
    DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 6680.89 8549.44 1.27969
    PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 1.20885
    Subtracted EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 4068.56 5252.6 1184.04
    HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted 108.653 100.352 8.301
    POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked 242.691 265.481 22.79

    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/