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 273 to 322 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    273 WASF3 wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 12748.1 11770.9 1.08302
    274 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 10432.4 11298.4 1.08301
    275 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 10783 11674.1 1.08264
    276 no value 60s ribosomal protein l9. [swissprot;acc:p32969] 10741.6 9922.33 1.08257
    277 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 11096.8 10251.6 1.08245
    278 STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11644 10763.4 1.08181
    279 ANAPC11 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 10614.2 9812.39 1.08171
    280 CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 10620.1 11471.2 1.08014
    281 no value phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 12522.7 13514.5 1.0792
    282 SH3GL1 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 8095.69 8732.68 1.07868
    283 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 11107.1 11959.2 1.07672
    284 TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 14898.9 16041.6 1.0767
    285 no value dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 10686 9925.58 1.07661
    286 DKC1 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 12228.2 11367.3 1.07573
    287 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 17842.7 16590.3 1.07549
    288 TYRP1 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 14930.6 16053 1.07517
    289 FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 15147.2 14091.9 1.07489
    290 no value interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
    291 FUBP1 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 10922.9 11731.8 1.07406
    292 no value ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 10280.5 9574.98 1.07368
    293 10287.1 9583.27 1.07344
    294 TAF12 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 13981.5 13025.1 1.07343
    295 no value transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 13687.7 12751.8 1.07339
    296 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 10194.1 10941.8 1.07335
    297 DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 8123.75 8719 1.07327
    298 no value 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 11977.8 12842.5 1.07219
    299 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 12338.7 11512.3 1.07178
    300 PRKACG camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 9270.49 8650.24 1.0717
    301 SH2B1 sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 12783 13698 1.07158
    302 no value guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] 7386.71 6895.44 1.07125
    303 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 11431.4 12244.1 1.07109
    304 sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 8021.78 7496.8 1.07003
    305 microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] 9431 8815 1.06988
    306 MLXIPL williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] 5540 5921 1.06877
    307 no value ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 1091 1021 1.06856
    308 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 11414.1 12191.8 1.06814
    309 LBP lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 13651 14572 1.06747
    310 no value glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 9328.78 8741.55 1.06718
    311 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 10253.5 9622.45 1.06558
    312 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 11959.8 12731.1 1.06449
    313 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 11935.6 12698.9 1.06395
    314 CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 10301.4 10957.5 1.06369
    315 RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 12121.6 12887.6 1.06319
    316 no value dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 10768.5 11444 1.06273
    317 protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 19939 18778 1.06183
    318 TMOD3 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] 8918.54 9465.32 1.06131
    319 SNX9 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
    320 ARF3 adp-ribosylation factor 3. [swissprot;acc:p16587] 11627.8 10958.2 1.0611
    321 no value adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 11634.4 10989.9 1.05864
    322 HSD17B1 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]

    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/