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 network_comparison green
Results: HTML CSV LaTeX Showing element 2232 to 2281 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
network_comparison
green
140 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] Divided Measured High confidence 2760.28 1.31425 2100.27
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Subtracted Ranked 228.306 30.295 198.011
NEURL neuralized-like. [refseq;acc:nm_004210] Rooted Low confidence 61.317 5.0224 66.3394
PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared High confidence 86609.4 21374.9 65234.5
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Divided Ranked 59 1.20408 49
SLC16A5 monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Squared Low confidence 62486.3 1.13186 70725.6
SPOCK2 testican-2 precursor. [swissprot;acc:q92563] Ranked 220.222 1.06278 234.047
UBE1C ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Measured 7628.44 1.08944 8310.74
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted Rooted High confidence 39.9725 13.0248 52.9973
141 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Divided Ranked Low confidence 219.344 1.0621 206.52
CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared High confidence 81520.8 1.45084 56188.5
COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Subtracted Ranked 239.991 29.247 269.238
DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided Rooted Low confidence 65.6112 1.07004 70.2066
HBS1L hbs1-like. [refseq;acc:nm_006620] Subtracted Measured High confidence 2597.5 1899 698.5
MAK serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Rooted Low confidence 84.7778 5.0037 89.7815
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] Ranked 211.056 12.324 198.732
NHLH1 helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] Squared 55838.6 6639.2 49199.4
PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] High confidence 86600.9 21371 65229.9
REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided Rooted 55.6161 1.19989 66.7332
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Ranked 59 1.20408 49
SLC16A1 monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Squared Low confidence 62462.2 1.13172 70689.7
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Measured High confidence 4405.4 1.3125 5782.08
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Subtracted Rooted 105.205 12.9635 92.2415
T brachyury protein (t protein). [swissprot;acc:o15178] Divided Measured Low confidence 6171.76 1.08897 6720.84
VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 7354.65 710.43 8065.08
142 AADAT alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] Squared 59947 6602.6 66549.6
ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured 10392.7 709.14 9683.56
CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Divided Squared High confidence 81478.9 1.45044 56175.2
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted Rooted 105.205 12.9635 92.2415
ICK intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence 84.7145 4.9907 89.7052
JUND transcription factor jun-d. [swissprot;acc:p17535] Measured High confidence 5638.2 1885.19 7523.39
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] Divided Ranked Low confidence 211.056 1.06201 198.732
OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Measured 10803 1.08837 11757.7
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 9276.47 1.30832 7090.37
PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Subtracted Squared 86600.9 21371 65229.9
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided Rooted 55.6161 1.19989 66.7332
PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 65.6112 1.07004 70.2066
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted Ranked 211.056 12.324 198.732
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Divided High confidence 59 1.20408 49
SLC16A7 monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Squared Low confidence 62451.1 1.13166 70673.1
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted Ranked High confidence 239.99 29.244 269.234
143 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided Rooted Low confidence 71.2143 1.06952 76.1654
ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured High confidence 9275.1 1.30826 7089.65
ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 1.20408 49
CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted Measured 15427.2 1854.4 13572.8
CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared Low confidence 65119.3 6571 58548.3
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] Ranked 211.056 12.324 198.732
HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Divided Measured 10696.6 1.08815 11639.5
OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Subtracted Squared High confidence 86600.9 21371 65229.9
PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Divided 124319 1.43145 86848.2

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/