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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 251 to 300 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
126 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 191.688 179.639 1.06707
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 94 114 1.21277
127 CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 203.678 190.88 1.06705
128 STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] High confidence 94 114 1.21277
STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 1.06618
129 COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 220.969 235.572 1.06609
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 94 114 1.21277
130 ABRA striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence 225.495 211.529 1.06602
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] High confidence 94 114 1.21277
131 SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 294.053 242.562 1.21228
STRN4 striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 200.825 1.065
132 DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 220.268 206.997 1.06411
TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 350 290 1.2069
133 PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 220.268 206.997 1.06411
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 350 290 1.2069
134 DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
TAGLN transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Low confidence 218.561 205.431 1.06391
135 CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] High confidence 350 290 1.2069
TAGLN3 neuronal protein np25. [swissprot;acc:q9ui15] Low confidence 218.66 205.57 1.06368
136 CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] High confidence 350 290 1.2069
HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Low confidence 202.996 190.854 1.06362
137 no value testican-3 precursor. [swissprot;acc:q9bq16] 220.395 234.389 1.0635
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] High confidence 350 290 1.2069
138 no value transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 205.4 1.0631
PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence 194.372 234.204 1.20493
139 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 271.752 225.68 1.20415
SPOCK1 testican-1 precursor (spock protein). [swissprot;acc:q08629] Low confidence 220.254 234.111 1.06291
140 RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] High confidence 59 49 1.20408
SPOCK2 testican-2 precursor. [swissprot;acc:q92563] Low confidence 220.222 234.047 1.06278
141 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 219.344 206.52 1.0621
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] High confidence 59 49 1.20408
142 MAN1B1 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Low confidence 211.056 198.732 1.06201
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence 59 49 1.20408
143 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Low confidence 211.056 198.732 1.06201
144 FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 265.686 319.651 1.20312
145 KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 1.20293
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 211.056 198.732 1.06201
146 KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] High confidence 265.632 319.531 1.20291
NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Low confidence 226.892 213.661 1.06193
147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 50.7983 42.3003 1.2009
ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 219.273 206.507 1.06182
148 SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 210.579 198.33 1.06176
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] High confidence 296.677 247.559 1.19841
149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 210.579 198.33 1.06176
150 MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence 55 46 1.19565
PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 206.516 194.554 1.06148

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/