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 Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 930 to 979 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    930 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] PKM2 231.357 239.778 1.0364
    931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] BHLHB4 159.13 164.917 1.03637
    932 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] MTRF1L 225.939 218.013 1.03636
    933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] BHLHB5 159.165 164.951 1.03635
    934 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] NOL6 242.024 233.544 1.03631
    935 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] no value 232.473 224.372 1.03611
    936 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
    937 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] SF3A3 220.246 212.618 1.03588
    938 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] SF3A1
    939 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] BRCA1 216.501 224.27
    940 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] CAPNS1 212.442 205.088 1.03586
    941 swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] ARID1A 212.437 205.083
    942 grancalcin. [swissprot;acc:p28676] GCA 212.442 205.088
    943 sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI 205.087
    944 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] PDCD6 212.437 205.083
    945 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B 212.44 205.085
    946 histone h4. [swissprot;acc:p02304] no value 227.765 219.902 1.03576
    947 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] SORBS2 212.51 205.191 1.03567
    948 target of myb protein 1. [swissprot;acc:o60784] TOM1 217.254 209.824 1.03541
    949 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] no value 217.253 209.826 1.0354
    950 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] ERCC5 252.873 261.821 1.03539
    951 triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] TRIO 217.253 209.827
    952 target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] TOM1L2 217.252 209.83 1.03537
    953 polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] EXOSC10 198.494 205.466 1.03512
    954 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] GSTZ1 267.447 276.773 1.03487
    955 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] MRPL27 231.163 239.205 1.03479
    956 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] SORBS3 211.812 204.732 1.03458
    957 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF 129.913 134.399 1.03453
    958 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 129.921 134.406 1.03452
    959 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] no value 237.558 229.677 1.03431
    960 zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] ZRF1
    961 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] PPP2R5E 130.066 134.527 1.0343
    962 cyclin g2. [swissprot;acc:q16589] CCNG2
    963 cyclin g1 (cyclin g). [swissprot;acc:p51959] CCNG1
    964 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] PPP2R5A
    965 partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] PARD6G 211.987 204.964 1.03426
    966 tubby protein homolog. [swissprot;acc:p50607] TUB
    967 protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] PRKCI
    968 numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] NUMB
    969 tbc1 domain family member 5. [swissprot;acc:q92609] TBC1D5
    970 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] TULP1
    971 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] VPS29
    972 numb-like protein (numb-r). [swissprot;acc:q9y6r0] NUMBL
    973 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] TULP3
    974 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] VPS35
    975 protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] PRKCZ
    976 t-cell activation wd repeat protein. [refseq;acc:nm_139281] WDR36 243.34 235.322 1.03407
    977 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] PFDN5 228.953 221.421 1.03402
    978 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] no value
    979 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] BLOC1S1 202.027 195.386 1.03399

    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/