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 1051 to 1100 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    526 RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] High confidence 250.538 234.401 1.06884
    SLC2A9 solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [swissprot;acc:q9nrm0] Low confidence 205.549 199.117 1.0323
    527 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] High confidence 248.56 232.579 1.06871
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Low confidence 208.004 201.497 1.03229
    528 SLC2A2 solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [swissprot;acc:p11168] 205.543 199.115 1.03228
    YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] High confidence 222.146 237.393 1.06864
    529 DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
    RNF113B zinc finger protein 183-like 1. [refseq;acc:nm_178861] Low confidence 205.116 198.702 1.03228
    530 no value solute carrier family 2, facilitated glucose transporter, member 3 (glucose transporter type 3, brain). [swissprot;acc:p11169] 205.541 199.114
    LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] High confidence 227.483 212.994 1.06803
    531 PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 223.356 209.149 1.06793
    SLC2A4 solute carrier family 2, facilitated glucose transporter, member 4 (glucose transporter type 4, insulin-responsive). [swissprot;acc:p14672] Low confidence 205.54 199.114 1.03227
    532 SLC2A14 glucose transporter 14. [refseq;acc:nm_153449] 205.541 199.115
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] High confidence 250.942 235.004 1.06782
    533 SLC2A1 solute carrier family 2, facilitated glucose transporter, member 1 (glucose transporter type 1, erythrocyte/brain) (hepg2 glucose transporter). [swissprot;acc:p11166] Low confidence 205.533 199.112 1.03225
    SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] High confidence 250.942 235.004 1.06782
    534 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
    ZFAND5 zinc finger protein 216. [swissprot;acc:o76080] Low confidence 184.361 178.613 1.03218
    535 POLR2H dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] High confidence 236.662 252.708 1.0678
    ZFAND6 protein associated with prk1. [refseq;acc:nm_019006] Low confidence 184.361 178.613 1.03218
    536 RANBP9 ran binding protein 9; novel centrosomal protein ranbpm; ran binding protein, centrosomal. [refseq;acc:nm_005493] 203.519 197.195 1.03207
    SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] High confidence 242.531 227.136 1.06778
    537 DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 229.803 215.301 1.06736
    MEGF11 megf11 protein. [refseq;acc:nm_032445] Low confidence 207.951 201.517 1.03193
    538 MEGF10 megf10 protein. [refseq;acc:nm_032446] 207.949 1.03192
    POLR2L dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] High confidence 237.627 253.604 1.06724
    539 CRBN protein x 0001. [refseq;acc:nm_016302] Low confidence 199.661 193.489 1.0319
    MEMO1P protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] High confidence 236.964 252.86 1.06708
    540 SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    541 MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    542 INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    543 SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    544 INPP4A inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    545 EIF6 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] High confidence 248.866 233.287 1.06678
    RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Low confidence 202.949 196.678 1.03188
    546 TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
    WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence 207.222 194.262 1.06671
    547 CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 207.26 194.346 1.06645
    SESN3 sestrin 3. [swissprot;acc:p58005] Low confidence 203.305 197.023 1.03188
    548 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] High confidence 207.26 194.346 1.06645
    FLOT1 flotillin-1. [swissprot;acc:o75955] Low confidence 203.303 197.022 1.03188
    549 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] High confidence 207.26 194.346 1.06645
    SESN2 sestrin 2 (hi95). [swissprot;acc:p58004] Low confidence 203.306 197.024 1.03188
    550 HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] High confidence 207.26 194.346 1.06645
    SESN1 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Low confidence 203.299 197.018 1.03188

    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/