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.


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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
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
sedlin. [swissprot;acc:o14582] High confidence 129.219 121.261 1.06563
566 serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence 168.935 163.869 1.03091
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 129.219 121.261 1.06563
567 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] Low confidence 206.46 200.275 1.03088
bet3 homolog. [swissprot;acc:o43617] High confidence 129.219 121.261 1.06563
568 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Low confidence 202.86 196.783 1.03088
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] High confidence 226.3 212.38 1.06554
569 acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] Low confidence 206.46 200.275 1.03088
t54 protein. [swissprot;acc:q92917] High confidence 226.3 212.38 1.06554
570 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] Low confidence 206.46 200.275 1.03088
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] High confidence 229.709 215.631 1.06529
571 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Low confidence 206.46 200.275 1.03088
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] High confidence 238.529 254.099 1.06528
572 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] Low confidence 206.46 200.275 1.03088
cbf1 interacting corepressor. [refseq;acc:nm_004882] High confidence 227.86 213.945 1.06504
573 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] Low confidence 206.46 200.275 1.03088
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] High confidence 227.86 213.945 1.06504
574 nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Low confidence 202.855 196.78 1.03087
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] High confidence 221.807 208.264 1.06503
575 arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Low confidence 202.85 196.777 1.03086
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] High confidence 221.807 208.264 1.06503

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/