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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 451 to 500 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    451 polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] POLR3C 239.092 257.705 1.07785
    452 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value 224.161 207.972 1.07784
    453 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1
    454 40s ribosomal protein s26. [swissprot;acc:p02383] no value 210.224 226.578 1.07779
    455 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] TIMM22 210.225
    456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] ATPAF2
    457 ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] UQCRB
    458 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 235.922 218.925 1.07764
    459 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] BAG3 233.529 216.737 1.07748
    460 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] SF3A2 223.648 207.62 1.0772
    461 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] KLF5
    462 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] MKI67IP 254.434 236.224 1.07709
    463 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] POLR3F 238.921 257.327 1.07704
    464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] FNBP1 210.578 226.764 1.07686
    465 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] CHRNA7 248.152 267.226
    466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] ADCY6
    467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] ADCY5
    468 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] LRRC15
    469 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] FEM1B
    470 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] LRRC3
    471 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] LAMC1
    472 thymic stromal co-transporter. [refseq;acc:nm_033051] SLC46A2
    473 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 225.661 209.651 1.07637
    474 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] KCNA2 226.789 210.818 1.07576
    475 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] KCNA1 226.727 210.816 1.07547
    476 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] KCNA4 226.681 210.814 1.07527
    477 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] NIP7 251.926 234.547 1.0741
    478 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 228.051 212.321 1.07409
    479 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] NOLA1
    480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] NETO2 237.109 254.667 1.07405
    481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] NETO1
    482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] HNRNPU
    483 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
    484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] HNRPUL1
    485 60s ribosomal protein l18. [swissprot;acc:q07020] RPL18
    486 mct-1 protein. [refseq;acc:nm_014060] MCTS1 226.313 243.03 1.07387
    487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] MRPL22
    488 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 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
    490 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] ARHGEF7 220.183 236.015 1.0719
    491 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 251.83 234.951 1.07184
    492 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 220.171 235.979 1.0718
    493 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] COG5 220.172 235.98
    494 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] PAK1
    495 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] PAK3 220.171 235.979
    496 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 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
    498 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] ARHGEF6 220.161 235.95 1.07172
    499 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] TPI1 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

    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/