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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Gene Filtered Network Comparison Type Value Type network_comparison Interaction Map Rank green red description
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 77072 in total
Filtered  : 0
Network Comparison Type  : Divided
Value Type  : Squared
network_comparison
Interaction Map
Rank
green
red
description
1.45875 Low confidence 169 802.961 1171.32 alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279]
1.45943 168 150.972 220.333 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]
1.4611 167 5345.62 7810.49 small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]
1.46537 High confidence 185 0.0854438 0.125207 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]
Low confidence 166
1.47582 165 7081.4 10450.9 fos-related antigen 2. [swissprot;acc:p15408]
1.47811 High confidence 184 2.86829 4.23965 transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
1.47937 183 56.1843 37.9786 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]
1.47947 Low confidence 164 147.643 218.433 transcription factor bteb4 (basic transcription element binding- protein 4) (bte-binding protein 4) (krueppel-like factor 16) (novel sp1-like zinc finger transcription factor 2) (transcription factor nslp2). [swissprot;acc:q9bxk1]
1.47953 163 1929.49 1304.12 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]
1.4848 162 7967.67 5366.16 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]
1.49026 High confidence 182 482.631 323.856 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
1.49065 Low confidence 161 59791.4 40110.9 ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]
1.49232 High confidence 181 210.151 140.822 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]
Low confidence 160
1.49332 High confidence 180 25982 38799.5 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]
1.49742 179 0.426714 0.284967 suppressor of actin 1. [refseq;acc:nm_014016]
1.49759 Low confidence 159 7596.22 11376 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]
1.50019 High confidence 177 109.766 73.1683 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]
178 dc11 protein. [refseq;acc:nm_020186]
Low confidence 157 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]
158 dc11 protein. [refseq;acc:nm_020186]
1.50186 156 7.23384 4.8166 williams beuren syndrome chromosome region 21 isoform 1. [refseq;acc:nm_148912]
1.50384 155 236.017 156.943 dead-box protein. [refseq;acc:nm_018665]
1.5131 154 13132.7 8679.33 glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]
1.52379 153 955.944 627.347 bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2]
1.52448 152 2121.73 1391.77 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]
1.54359 151 209.689 135.845 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]
1.55954 High confidence 175 75.7214 48.5538 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
176 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
1.5596 174 75.3968 48.3438 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]
1.55963 173 75.2348 48.239 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
1.55986 172 74.0536 47.4746 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]
1.5625 Low confidence 150 2.13609 1.3671 protein c20orf142 precursor. [swissprot;acc:q8n6m3]
1.5628 High confidence 171 2488.07 1592.06 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]
1.56969 Low confidence 149 2474.6 1576.49
1.57726 High confidence 170 276.854 175.528 calcyphosine. [swissprot;acc:q13938]
1.58189 169 8.90793 14.0914 gaba-a receptor-associated protein. [sptrembl;acc:q9by60]
1.58656 168 213.584 338.863 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
1.58702 Low confidence 148 157.837 250.49
1.58925 High confidence 167 105.991 168.446 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]
1.58979 Low confidence 147 352.514 221.736 rho guanine nucleotide exchange factor (gef) 12; leukemia-associated rho guanine nucleotide exchange factor. [refseq;acc:nm_015313]
1.59322 High confidence 166 350.57 220.039 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]
1.59894 165 34012.2 54383.4 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
1.60218 164 91.0551 145.887 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]
1.6022 163 3165.6 5071.93 p28 ing5. [refseq;acc:nm_032329]
1.62716 157 3763.18 6123.28 udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]
158 udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]
159 udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]
160 glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]

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/