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 Network Comparison Type Gene Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 951 to 1000 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    476 FUCA1 tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Low confidence 202.271 195.742 1.03336
    KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] High confidence 226.681 210.814 1.07527
    477 HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Low confidence 203.823 197.249 1.03333
    NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 251.926 234.547 1.0741
    478 BLVRB flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [swissprot;acc:p30043] Low confidence 207.68 214.591 1.03328
    BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] High confidence 228.051 212.321 1.07409
    479 NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
    VTA1 protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] Low confidence 207.68 214.591 1.03328
    480 NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] High confidence 237.109 254.667 1.07405
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Low confidence 203.822 197.259 1.03327
    481 NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] High confidence 237.109 254.667 1.07405
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 171.564 166.045 1.03324
    482 HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] High confidence 237.109 254.667 1.07405
    TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Low confidence 204.65 198.086 1.03314
    483 no value rna-binding protein. [refseq;acc:nm_019027] 203.821 197.289 1.03311
    RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] High confidence 237.109 254.667 1.07405
    484 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Low confidence 203.821 197.291 1.0331
    HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] High confidence 237.109 254.667 1.07405
    485 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Low confidence 205.109 198.551 1.03303
    RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] High confidence 237.109 254.667 1.07405
    486 CXorf9 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] Low confidence 204.331 211.075 1.03301
    MCTS1 mct-1 protein. [refseq;acc:nm_014060] High confidence 226.313 243.03 1.07387
    487 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Low confidence 206.763 200.18 1.03289
    MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] High confidence 226.313 243.03 1.07387
    488 SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 225.026 209.798 1.07258
    TMOD4 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Low confidence 209.136 202.478 1.03288
    489 PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] High confidence 231.276 215.627 1.07257
    TMOD3 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Low confidence 209.136 202.478 1.03288
    490 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] High confidence 220.183 236.015 1.0719
    TMOD1 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Low confidence 209.136 202.478 1.03288
    491 GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] High confidence 251.83 234.951 1.07184
    SNX9 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Low confidence 209.136 202.478 1.03288
    492 PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] High confidence 220.171 235.979 1.0718
    TMOD2 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Low confidence 209.136 202.478 1.03288
    493 COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 235.98 1.0718
    TNK2 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Low confidence 209.136 202.478 1.03288
    494 EEF1B2 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] 206.154 199.596 1.03286
    PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] High confidence 220.172 235.98 1.0718
    495 LIMD1 lim domains containing 1. [refseq;acc:nm_014240] Low confidence 203.117 196.671 1.03278
    PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] High confidence 220.171 235.979 1.0718
    496 no value probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Low confidence 203.117 196.671 1.03278
    PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 250.938 234.134 1.07177
    497 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Low confidence 203.117 196.671 1.03278
    498 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] High confidence 220.161 235.95 1.07172
    KIFAP3 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] Low confidence 203.117 196.671 1.03278
    499 POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 203.167 196.732 1.03271
    TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] High confidence 231.496 248.048 1.0715
    500 ING2 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
    RCL1 rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Low confidence 203.85 197.403 1.03266

    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/