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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 908 to 957 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    454 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Low confidence 210.252 203.24 1.0345
    455 CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 210.251 203.241 1.03449
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] High confidence 210.225 226.578 1.07779
    456 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
    CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Low confidence 210.251 203.241 1.03449
    457 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]
    UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] High confidence 210.225 226.578 1.07779
    458 AP1B1 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Low confidence 206.948 200.058 1.03444
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 235.922 218.925 1.07764
    459 BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 233.529 216.737 1.07748
    GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Low confidence 207.797 214.954 1.03444
    460 no value proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602] 209.188 202.243 1.03434
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] High confidence 223.648 207.62 1.0772
    461 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]
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 201.429 194.776 1.03416
    462 MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 254.434 236.224 1.07709
    SLC7A5 large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] Low confidence 201.466 194.819 1.03412
    463 POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] High confidence 238.921 257.327 1.07704
    PRRX1 paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821] Low confidence 194.41 201.036 1.03408
    464 ELL2 rna polymerase ii elongation factor ell2. [swissprot;acc:o00472] 198.618 205.369 1.03399
    FNBP1 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] High confidence 210.578 226.764 1.07686
    465 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 248.152 267.226
    HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Low confidence 207.812 200.994 1.03392
    466 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] High confidence 248.152 267.226 1.07686
    HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Low confidence 207.812 200.994 1.03392
    467 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 248.152 267.226 1.07686
    HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Low confidence 207.812 200.994 1.03392
    468 HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
    LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 248.152 267.226 1.07686
    469 DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Low confidence 207.812 200.994 1.03392
    FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] High confidence 248.152 267.226 1.07686
    470 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Low confidence 198.464 191.96 1.03388
    LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 248.152 267.226 1.07686
    471 LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
    RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Low confidence 208.29 201.499 1.0337
    472 PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 201.847 195.283 1.03361
    SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 248.152 267.226 1.07686
    473 EXOC1 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Low confidence 209.111 202.34 1.03346
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 225.661 209.651 1.07637
    474 KCNA2 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 226.789 210.818 1.07576
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 171.213 165.68 1.0334
    475 FUCA2 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] 202.311 195.778 1.03337
    KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] High confidence 226.727 210.816 1.07547
    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]

    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/