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 description Hugo Network Comparison Type 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
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    476 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] KCNA4 High confidence 226.681 210.814 1.07527
    tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] FUCA1 Low confidence 202.271 195.742 1.03336
    477 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR 203.823 197.249 1.03333
    saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] NIP7 High confidence 251.926 234.547 1.0741
    478 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] BLVRB Low confidence 207.68 214.591 1.03328
    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] BRF1 High confidence 228.051 212.321 1.07409
    479 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] NOLA1
    protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] VTA1 Low confidence 207.68 214.591 1.03328
    480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] NETO2 High confidence 237.109 254.667 1.07405
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Low confidence 203.822 197.259 1.03327
    481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] NETO1 High confidence 237.109 254.667 1.07405
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Low confidence 171.564 166.045 1.03324
    482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] HNRNPU High confidence 237.109 254.667 1.07405
    thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] TRIP12 Low confidence 204.65 198.086 1.03314
    483 rna-binding protein. [refseq;acc:nm_019027] no value 203.821 197.289 1.03311
    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] RUNX2 High confidence 237.109 254.667 1.07405
    484 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Low confidence 203.821 197.291 1.0331
    e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] HNRPUL1 High confidence 237.109 254.667 1.07405
    485 60s ribosomal protein l18. [swissprot;acc:q07020] RPL18
    tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] BRPF1 Low confidence 205.109 198.551 1.03303
    486 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] CXorf9 204.331 211.075 1.03301
    mct-1 protein. [refseq;acc:nm_014060] MCTS1 High confidence 226.313 243.03 1.07387
    487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] MRPL22
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 Low confidence 206.763 200.18 1.03289
    488 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] TMOD4 209.136 202.478 1.03288
    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] SART1 High confidence 225.026 209.798 1.07258
    489 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] PPM1B 231.276 215.627 1.07257
    ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] TMOD3 Low confidence 209.136 202.478 1.03288
    490 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] ARHGEF7 High confidence 220.183 236.015 1.0719
    tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] TMOD1 Low confidence 209.136 202.478 1.03288
    491 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 High confidence 251.83 234.951 1.07184
    sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] SNX9 Low confidence 209.136 202.478 1.03288
    492 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] TMOD2
    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] PAK2 High confidence 220.171 235.979 1.0718
    493 activated p21cdc42hs kinase. [refseq;acc:nm_005781] TNK2 Low confidence 209.136 202.478 1.03288
    conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] COG5 High confidence 220.172 235.98 1.0718
    494 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] EEF1B2 Low confidence 206.154 199.596 1.03286
    serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] PAK1 High confidence 220.172 235.98 1.0718
    495 lim domains containing 1. [refseq;acc:nm_014240] LIMD1 Low confidence 203.117 196.671 1.03278
    serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] PAK3 High confidence 220.171 235.979 1.0718
    496 probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] no value Low confidence 203.117 196.671 1.03278
    suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 High confidence 250.938 234.134 1.07177
    497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] EBNA1BP2 251.344 234.514
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Low confidence 203.117 196.671 1.03278
    498 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] KIFAP3
    rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] ARHGEF6 High confidence 220.161 235.95 1.07172
    499 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI Low confidence 203.167 196.732 1.03271
    triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] TPI1 High confidence 231.496 248.048 1.0715
    500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] ING2 224.662 240.673 1.07127
    rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] RCL1 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/