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 Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2208 to 2257 of 14920 in total
    Interaction Map	High confidence
    Network Comparison Type Divided
    Rank description Value Type Filtered red green network_comparison 276 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37] Measured 1 3119.98 2579.49 1.20953 277 40s ribosomal protein s29. [source:swissprot;acc:p30054] Ranked 1 241.849 267.642 1.10665 277 60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621] Ranked 0 11096.8 10251.6 1.08245 277 adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328] Rooted 0 24.1033 22.0791 1.09168 277 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6] Measured 0 870.93 975.647 1.12024 277 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491] Squared 0 21885.1 17682.1 1.2377 277 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [source:swissprot;acc:o76081] Measured 1 3119.98 2579.49 1.20953 277 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424] Rooted 1 65.9938 73.9449 1.12048 277 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621] Squared 1 16120.1 20665.7 1.28198 278 40s ribosomal protein s11. [source:swissprot;acc:p04643] Ranked 1 241.399 267.088 1.10642 278 associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799] Ranked 0 11644 10763.4 1.08181 278 bystin. [source:swissprot;acc:q13895] Squared 0 26569.7 32857.7 1.23666 278 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247] Rooted 0 34.0153 31.1803 1.09092 278 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333] Squared 1 16120.1 20665.7 1.28198 278 ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464] Rooted 1 65.9938 73.9449 1.12048 278 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513] Measured 0 2162.33 1932 1.11922 278 transcription factor lbx1. [source:swissprot;acc:p52954] Measured 1 3119.98 2579.49 1.20953 279 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5] Ranked 0 10614.2 9812.39 1.08171 279 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [source:refseq;acc:nm_006614] Measured 0 545.902 610.424 1.11819 279 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658] Rooted 0 33.1655 30.4161 1.09039 279 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7] Squared 0 229.508 283.721 1.23621 279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576] Ranked 1 252.644 228.42 1.10605 279 mosaic protein lgn. [source:swissprot;acc:p81274] Measured 1 3119.98 2579.49 1.20953 279 musashi 2 isoform a. [source:refseq;acc:nm_138962] Squared 1 15569.5 19953.6 1.28158 279 neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401] Rooted 1 66.0989 74.0609 1.12046 280 ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9] Squared 0 29812 36822.7 1.23516 280 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36] Rooted 1 57.9068 64.8562 1.12001 280 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132] Rooted 0 28.8531 26.484 1.08945 280 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0] Ranked 0 10620.1 11471.2 1.08014 280 metastasis-associated protein mta1. [source:swissprot;acc:q13330] Ranked 1 252.512 228.356 1.10578 280 musashi 1. [source:refseq;acc:nm_002442] Squared 1 15569.5 19953.6 1.28158 280 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [source:swissprot;acc:p32004] Measured 0 545.902 610.424 1.11819 280 regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6] Measured 1 3119.98 2579.49 1.20953 281 60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621] Ranked 1 241.808 267.335 1.10557 281 guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471] Measured 1 3119.98 2579.49 1.20953 281 nuclear protein ukp68. [source:refseq;acc:nm_024824] Squared 1 15569.5 19953.6 1.28158 281 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6] Ranked 0 12522.7 13514.5 1.0792 281 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322] Squared 0 4275.32 3463.45 1.23441 281 suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169] Rooted 0 27.1299 29.5494 1.08918 281 transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [source:swissprot;acc:q16594] Measured 0 545.902 610.424 1.11819 281 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661] Rooted 1 57.9068 64.8562 1.12001 282 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). [source:swissprot;acc:q09028] Ranked 1 252.39 228.297 1.10553 282 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708] Rooted 0 25.5082 23.4377 1.08834 282 pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790] Measured 0 178.955 199.751 1.11621 282 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361] Squared 0 8755.38 7114.89 1.23057 282 rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736] Measured 1 3119.98 2579.49 1.20953 282 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961] Ranked 0 8095.69 8732.68 1.07868 282 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428] Rooted 1 57.9819 64.9302 1.11984 282 stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975] Squared 1 59704 76460.4 1.28066 283 60s ribosomal protein l11. [source:swissprot;acc:p39026] Ranked 1 241.828 267.346 1.10552 Legend: - Rank is the rank after comparing the two networks - 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/