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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3836 to 3885 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
959 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Rooted 62.1275 65.7481 1.05828
960 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Squared 29830.2 34375.9 1.15239
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Rooted 66.4035 70.2633 1.05813
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 10733.2 1.09688
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Ranked 237.558 229.677 1.03431
961 peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured 11773 10733.2 1.09688
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Rooted 98.7609 93.3602 1.05785
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Squared 29830.2 34375.9 1.15239
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Ranked 130.066 134.527 1.0343
962 cyclin g2. [swissprot;acc:q16589]
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] Squared 29830.2 34375.9 1.15239
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Rooted 57.5529 60.879 1.05779
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Measured 11773 10733.2 1.09688
963 cyclin g1 (cyclin g). [swissprot;acc:p51959] Ranked 130.066 134.527 1.0343
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Measured 11773 10733.2 1.09688
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Rooted 57.5529 60.879 1.05779
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Squared 23594.2 27188.9 1.15236
964 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Measured 11773 10733.2 1.09688
inositol polyphosphate multikinase. [refseq;acc:nm_152230] Squared 22271.9 25656.8 1.15198
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Rooted 52.9804 50.0947 1.0576
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Ranked 130.066 134.527 1.0343
965 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Squared 22271.9 25656.8 1.15198
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Rooted 52.9804 50.0947 1.0576
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Ranked 211.987 204.964 1.03426
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Measured 11773.7 10733.8 1.09688
966 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Squared 22271.9 25656.8 1.15198
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Measured 7817.9 8575.12 1.09686
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Rooted 52.9804 50.0947 1.0576
tubby protein homolog. [swissprot;acc:p50607] Ranked 211.987 204.964 1.03426
967 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Squared 25580.6 29466.1 1.15189
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Measured 7813.35 8569.96 1.09684
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Ranked 211.987 204.964 1.03426
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Rooted 52.9804 50.0947 1.0576
968 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Squared 25580.6 29466.1 1.15189
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Ranked 211.987 204.964 1.03426
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Measured 7813.48 8570.11 1.09684
969 60s ribosomal protein l18. [swissprot;acc:q07020] Rooted 52.9804 50.0947 1.0576
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Measured 7813.34 8569.95 1.09684
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Squared 19488.7 22447.5 1.15182
tbc1 domain family member 5. [swissprot;acc:q92609] Ranked 211.987 204.964 1.03426
970 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Measured 7813.45 8570.07 1.09684
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Squared 24426.8 28125 1.1514
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Rooted 61.6649 65.1892 1.05715
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Ranked 211.987 204.964 1.03426
971 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Rooted 61.6649 65.1892 1.05715
acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Squared 27478.1 31623.7 1.15087
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Measured 7813.36 8569.97 1.09684
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Ranked 211.987 204.964 1.03426
972 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Rooted 61.6649 65.1892 1.05715

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/