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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2901 to 2950 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    182 Divided HAT1 Ranked histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] High confidence 277.546 1.15422 240.461
    NUBP2 Rooted nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Low confidence 69.7469 1.06274 74.1228
    PRKAG1 Squared 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 54678.1 1.11042 49240.7
    PXK Ranked px serine/threonine kinase. [refseq;acc:nm_017771] 196.372 1.05385 206.947
    Subtracted no value rd protein. [swissprot;acc:p18615] High confidence 227.357 26.793 254.15
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Low confidence 211.475 10.702 222.177
    JPH3 Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 57.5193 4.4228 53.0965
    LIPM Squared ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 54471.8 5179.4 49292.4
    MSI1 Measured musashi 1. [refseq;acc:nm_002442] High confidence 4241.57 1569.22 5810.79
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Low confidence 5334.13 599.27 5933.4
    RBM15B Rooted chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] High confidence 47.6504 10.72 36.9304
    SFRS8 Squared splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] 64739.9 14439.3 50300.6
    183 Divided no value Measured apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 4069.83 1.29051 5252.17
    Ranked bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Low confidence 196.372 1.05385 206.947
    ACADVL Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] High confidence 79779.8 1.35478 108084
    ATP1B1 sodium/potassium-transporting atpase beta-1 chain (sodium/potassium- dependent atpase beta-1 subunit). [swissprot;acc:p05026] Low confidence 52767.9 1.11042 47520.7
    DNALI1 Rooted axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 67.0706 1.06257 71.2671
    NCBP2 Ranked 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 228.306 1.153 198.011
    NEDD9 Rooted enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 57.4586 1.15446 66.3336
    PBLD Measured mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Low confidence 10087.8 1.07763 10870.9
    Subtracted ANAPC2 Squared anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] High confidence 69124.3 14226.9 54897.4
    GSTO1 Ranked glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 26.793 254.15
    HSPB6 heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Low confidence 219.606 10.702 208.904
    JPH2 Rooted junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 57.5193 4.4228 53.0965
    MFAP4 Measured microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 5334.13 599.27 5933.4
    PAPOLG Squared poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 51730.2 5171 46559.2
    RGS19 Rooted regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] High confidence 47.6504 10.72 36.9304
    ZC3H14 Measured nuclear protein ukp68. [refseq;acc:nm_024824] 4241.57 1569.22 5810.79
    184 Divided no value spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Low confidence 7764.08 1.07749 8365.72
    Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] High confidence 72886.3 1.35203 98544.5
    ATG4A Rooted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 153.602 1.15321 133.195
    OSR1 Ranked odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 1.15239 237.79
    SNRPB2 Rooted u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Low confidence 70.6712 1.06257 75.0934
    SRM Squared spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] 54936 1.11039 49474.7
    SYNCRIP Measured ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 4069.83 1.29051 5252.17
    TSGA10 Ranked testis specific, 10. [refseq;acc:nm_025244] Low confidence 196.373 1.05384 206.946
    Subtracted AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] High confidence 227.357 26.793 254.15
    CLEC3B Measured tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 10804.7 1558.9 12363.6
    CRYAA Ranked alpha crystallin a chain. [swissprot;acc:p02489] Low confidence 219.589 10.694 208.895
    PC Squared pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] High confidence 48127.9 14117.7 62245.6
    PPP1R14D Measured protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Low confidence 5334.13 599.27 5933.4
    RBM15 Rooted putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] High confidence 47.6504 10.72 36.9304
    SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Low confidence 57.5193 4.4228 53.0965
    TMF1 Squared tata element modulatory factor (tmf). [swissprot;acc:p82094] 54650.6 5149.1 49501.5
    185 Divided no value Measured putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 6852.7 1.07736 6360.64
    Ranked f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 212.589 1.0537 201.755
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] High confidence 281.582 1.14292 246.371
    HNRNPR Measured heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 4069.83 1.29051 5252.17
    HS3ST6 Squared c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 41502.9 1.34589 30836.8
    MAP1LC3B Rooted microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 153.578 1.1532 133.176

    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/