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 network_comparison green
    Results: HTML CSV LaTeX Showing element 2130 to 2179 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    267 no value estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Squared Subtracted 59334.6 8705.5 68040.1
    ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted Divided 66.1064 1.12103 74.1073
    CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Measured Subtracted 11222.2 1273.27 9948.93
    DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked Divided 241.07 1.11121 267.88
    LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 26157.6 1.29261 20236.2
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 14021.4 1.21682 11523
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Subtracted 61.2893 9.0963 70.3856
    268 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Divided 66.1064 1.12103 74.1074
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured 24473.9 1.21593 20127.8
    CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Subtracted 11222.2 1273.27 9948.93
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked Divided 271.016 1.10996 244.167
    LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 26157.6 1.29261 20236.2
    PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked Subtracted 241.625 23.511 265.136
    SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared 35533.9 8693.1 44227
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 61.2893 9.0963 70.3856
    269 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Ranked 241.625 23.511 265.136
    ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared 35508.7 8682.7 44191.4
    BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured 4808.79 1265.42 6074.21
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Rooted 61.2893 9.0963 70.3856
    HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 66.1064 1.12103 74.1074
    LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 4590.18 1.21466 5575.52
    PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked 241.373 1.10763 267.352
    SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 26157.6 1.29261 20236.2
    270 C16orf80 transcription factor iib. [refseq;acc:nm_013242] 64739.9 1.28706 50300.6
    CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured Subtracted 4810.22 1264.82 6075.04
    CRKL crk-like protein. [swissprot;acc:p46109] Rooted Divided 66.1064 1.12103 74.1074
    FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 1.21358 19479.8
    FLAD1 fad synthetase. [refseq;acc:nm_025207] Ranked 241.373 1.10763 267.352
    HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared Subtracted 35508.6 8682.7 44191.3
    RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 241.612 23.507 265.119
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 9.007 39.0445
    271 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked Divided 241.373 1.10763 267.352
    ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 66.1064 1.12103 74.1073
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 2554.89 1.21092 3093.78
    COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared Subtracted 53774.6 8669.1 45105.5
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 8.9859 53.7761
    NEDD9 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] Measured 4812.01 1264.08 6076.09
    SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 23.487 266.559
    SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared Divided 64739.9 1.28706 50300.6
    272 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Rooted Subtracted 57.4432 8.8875 66.3307
    FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared Divided 36563.7 1.28464 46971.1
    FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 1.12103 74.1074
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured 3858.52 1.21012 4669.27
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked 241.373 1.10763 267.352
    MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 23.418 266.248
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured 1991.03 1230.35 3221.38
    SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared 35247.5 8573 43820.5
    273 AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 30826.5 8557.4 39383.9
    CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Rooted 57.45 8.882 66.332
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured Divided 3199.4 1.20985 3870.8

    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/