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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2201 to 2250 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
551 AP1M2 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] Divided Low confidence 205.768 199.453 1.03166
GRAP2 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
GYG1 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Subtracted Low confidence 200.014 193.745 6.269
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 13.955
552 CRKL crk-like protein. [swissprot;acc:p46109] Divided 207.26 194.346 1.06645
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Low confidence 203.511 197.267 1.03165
Subtracted 6.244
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 13.955
553 no value putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 226.3 212.38 13.92
ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Divided 207.26 194.346 1.06645
AP1M1 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] Low confidence 205.75 199.452 1.03158
SSRP1 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] Subtracted 205.184 198.948 6.236
554 ERGIC2 cda14. [refseq;acc:nm_016570] 211.525 205.3 6.225
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided High confidence 207.26 194.346 1.06645
GPKOW t54 protein. [swissprot;acc:q92917] Subtracted 226.3 212.38 13.92
NUTF2 nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] Divided Low confidence 205.57 199.279 1.03157
555 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Subtracted High confidence 227.86 213.945 13.915
ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Low confidence 207.131 200.94 6.191
CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Divided 201.554 195.387 1.03156
FGR 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 ANP32C acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] Subtracted Low confidence 206.46 200.275 6.185
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Divided High confidence 207.27 194.368 1.06638
GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Subtracted 227.86 213.945 13.915
MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Divided Low confidence 206.737 200.417 1.03153
557 ANP32A 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] Subtracted 206.46 200.275 6.185
CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided High confidence 207.272 194.371 1.06637
DNAJB11 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] Low confidence 206.737 200.417 1.03153
SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Subtracted High confidence 216.557 230.362 13.805
558 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 248.994 235.255 13.739
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 135.087 144.041 1.06628
ANP32D acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] Subtracted Low confidence 206.46 200.275 6.185
HTATSF1 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Divided 209.347 202.978 1.03138
559 RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Subtracted High confidence 216.72 230.439 13.719
SSRP1 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] Divided Low confidence 205.184 198.948 1.03134
USO1 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Subtracted 206.46 200.275 6.185
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided High confidence 207.309 194.452 1.06612
560 ANP32B acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] Subtracted Low confidence 206.46 200.275 6.185
DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] High confidence 232.118 218.406 13.712
GYG2 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Divided Low confidence 199.227 193.173 1.03134
SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] High confidence 205.74 193.021 1.06589
561 no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Subtracted 228.215 214.546 13.669
ATP9A potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided Low confidence 202.845 209.189 1.03128
BRD8 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] Subtracted 206.46 200.275 6.185
SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Divided High confidence 205.89 193.183 1.06578
562 CRBN protein x 0001. [refseq;acc:nm_016302] Subtracted Low confidence 199.661 193.489 6.172
ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Divided 203.367 197.208 1.03123
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] High confidence 220.744 207.121 1.06577
PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Subtracted 224.606 210.944 13.662
563 CAPS calcyphosine. [swissprot;acc:q13938] Divided 220.744 207.121 1.06577
CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Subtracted Low confidence 201.554 195.387 6.167

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/