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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1075 to 1124 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] POLR2L High confidence 237.627 253.604 1.06724
    megf10 protein. [refseq;acc:nm_032446] MEGF10 Low confidence 207.949 201.517 1.03192
    539 protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] MEMO1P High confidence 236.964 252.86 1.06708
    protein x 0001. [refseq;acc:nm_016302] CRBN Low confidence 199.661 193.489 1.0319
    540 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    541 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] MICAL2 High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    542 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] INPP4B High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    543 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] SEPHS1 High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    544 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] INPP4A High confidence 222.156 208.201 1.06703
    Low confidence 206.406 200.027 1.03189
    545 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] RPUSD2 202.949 196.678 1.03188
    eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] EIF6 High confidence 248.866 233.287 1.06678
    546 wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS 207.222 194.262 1.06671
    z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] TMBIM4 Low confidence 202.949 196.678 1.03188
    547 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK High confidence 207.26 194.346 1.06645
    sestrin 3. [swissprot;acc:p58005] SESN3 Low confidence 203.305 197.023 1.03188
    548 flotillin-1. [swissprot;acc:o75955] FLOT1 203.303 197.022
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2 High confidence 207.26 194.346 1.06645
    549 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value
    sestrin 2 (hi95). [swissprot;acc:p58004] SESN2 Low confidence 203.306 197.024 1.03188
    550 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] SESN1 203.299 197.018
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK High confidence 207.26 194.346 1.06645
    551 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] AP1M2 Low confidence 205.768 199.453 1.03166
    grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] GRAP2 High confidence 207.261 194.347 1.06645
    552 crk-like protein. [swissprot;acc:p46109] CRKL 207.26 194.346
    grb2-related adaptor protein. [swissprot;acc:q13588] GRAP Low confidence 203.511 197.267 1.03165
    553 adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] AP1M1 205.75 199.452 1.03158
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 High confidence 207.26 194.346 1.06645
    554 nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] NUTF2 Low confidence 205.57 199.279 1.03157
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN High confidence 207.26 194.346 1.06645
    555 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 Low confidence 201.554 195.387 1.03156
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR High confidence 207.26 194.346 1.06645
    556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 207.27 194.368 1.06638
    preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] MOBKL3 Low confidence 206.737 200.417 1.03153
    557 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] DNAJB11
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 High confidence 207.272 194.371 1.06637
    558 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] HTATSF1 Low confidence 209.347 202.978 1.03138
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value High confidence 135.087 144.041 1.06628
    559 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL 207.309 194.452 1.06612
    structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] SSRP1 Low confidence 205.184 198.948 1.03134
    560 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] GYG2 199.227 193.173
    son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] SOS1 High confidence 205.74 193.021 1.06589
    561 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] ATP9A Low confidence 202.845 209.189 1.03128
    son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] SOS2 High confidence 205.89 193.183 1.06578
    562 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] ECHS1 Low confidence 203.367 197.208 1.03123
    ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] GULP1 High confidence 220.744 207.121 1.06577

    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/