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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2708 to 2757 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    339 EVI1 ecotropic virus integration 1 site protein. [swissprot;acc:q03112] Squared Low confidence 53275.3 49485.7 1.07658
    GGPS1 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Ranked 209.518 201.554 1.03951
    HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Squared High confidence 46785.7 58383.2 1.24789
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured 20446.1 24136.4 1.18049
    IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Low confidence 9114.82 9621.71 1.05561
    340 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 20446.1 24136.4 1.18049
    nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Squared Low confidence 50915 47306.4 1.07628
    BET1L blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Ranked 201.827 194.178 1.03939
    CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Measured 8940.43 9437.54 1.0556
    MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] Ranked High confidence 235.383 258.476 1.09811
    PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 58.4926 64.8047 1.10791
    RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 71.2599 74.9558 1.05187
    RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared High confidence 32117 40054 1.24713
    341 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked 240.243 263.798 1.09805
    alpha-nac protein. [sptrembl;acc:q9h009] Squared Low confidence 50910.5 47302.9 1.07627
    ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Measured 7151 7548.35 1.05557
    BET1L blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Rooted 72.4676 76.2225 1.05181
    HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured High confidence 20446.1 24136.4 1.18049
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Ranked Low confidence 214.027 222.415 1.03919
    RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared High confidence 32056.4 39965.8 1.24673
    SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Rooted 51.9812 57.5858 1.10782
    342 no value tho complex 3. [refseq;acc:nm_032361] Ranked Low confidence 186.383 179.374 1.03907
    CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 70.4474 74.0813 1.05158
    DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Squared 50908.3 47301 1.07626
    EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Rooted High confidence 49.2715 54.5757 1.10765
    HGS hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared 70830.5 56822 1.24653
    HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured 20446.1 24136.4 1.18049
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Low confidence 7309.92 7715.51 1.05548
    RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Ranked High confidence 243.5 267.21 1.09737
    343 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Rooted 50.3169 45.4333 1.10749
    ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Measured Low confidence 7155.19 7551.48 1.05538
    COG7 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared High confidence 70830.5 56822 1.24653
    DIRAS2 di-ras2. [refseq;acc:nm_017594] Low confidence 50908.1 47300.9 1.07626
    HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured High confidence 20446.1 24136.4 1.18049
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked Low confidence 213.982 222.326 1.03899
    PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] High confidence 241.625 265.136 1.0973
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Rooted Low confidence 71.3123 74.9882 1.05155
    344 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Ranked High confidence 241.625 265.136 1.0973
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 20446.1 24136.4 1.18049
    CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Low confidence 8926.58 9420 1.05528
    IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Squared High confidence 37226.9 46400.1 1.24641
    MRPL44 mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] Ranked Low confidence 216.283 208.173 1.03896
    PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted High confidence 49.4233 54.7327 1.10743
    TM9SF3 transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45] Squared Low confidence 49200 45726.8 1.07596
    XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Rooted 68.8797 72.4244 1.05146
    345 CASP7 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Squared 49625.1 46146.2 1.07539
    CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Measured 8919.45 9410.98 1.05511
    CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked High confidence 242.14 265.697 1.09729
    DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted 56.2615 62.2958 1.10725
    HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 1.18049

    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/