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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1080 to 1129 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
540 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Low confidence 206.406 200.027 1.03189
541 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 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] 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] 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] 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] 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] High confidence 248.866 233.287 1.06678
546 wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 207.222 194.262 1.06671
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Low confidence 202.949 196.678 1.03188
547 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] High confidence 207.26 194.346 1.06645
sestrin 3. [swissprot;acc:p58005] Low confidence 203.305 197.023 1.03188
548 flotillin-1. [swissprot;acc:o75955] 203.303 197.022
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 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]
sestrin 2 (hi95). [swissprot;acc:p58004] Low confidence 203.306 197.024 1.03188
550 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 203.299 197.018
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
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] 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] High confidence 207.261 194.347 1.06645
552 crk-like protein. [swissprot;acc:p46109] 207.26 194.346
grb2-related adaptor protein. [swissprot;acc:q13588] 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] 205.75 199.452 1.03158
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] High confidence 207.26 194.346 1.06645
554 nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] 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] High confidence 207.26 194.346 1.06645
555 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 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] High confidence 207.26 194.346 1.06645
556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 207.27 194.368 1.06638
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 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]
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 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] Low confidence 209.347 202.978 1.03138
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] High confidence 135.087 144.041 1.06628
559 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 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] Low confidence 205.184 198.948 1.03134
560 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 199.227 193.173
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] High confidence 205.74 193.021 1.06589
561 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Low confidence 202.845 209.189 1.03128
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 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] Low confidence 203.367 197.208 1.03123
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] High confidence 220.744 207.121 1.06577
563 calcyphosine. [swissprot;acc:q13938]
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Low confidence 203.155 197.018 1.03115
564 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 203.197 197.076 1.03106
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] High confidence 220.744 207.121 1.06577
565 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Low confidence 203.157 197.064 1.03092

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
- 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/