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 11714 to 11763 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
963 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Measured Subtracted 5778.65 6328.56 549.91
cyclin g1 (cyclin g). [swissprot;acc:p51959] Ranked Divided 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
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Ranked Subtracted 219.656 212.547 7.109
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Rooted Divided 57.5529 60.879 1.05779
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 54.1622 57.6725 3.5103
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Squared Divided 23594.2 27188.9 1.15236
964 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Subtracted 24025.9 27585.7 3559.8
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted 54.1622 57.6725 3.5103
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Measured Divided 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
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Ranked Subtracted 219.656 212.547 7.109
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] Divided 130.066 134.527 1.0343
synapsin iii. [swissprot;acc:o14994] Measured Subtracted 5791.82 6340.86 549.04
965 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Squared Divided 22271.9 25656.8 1.15198
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Measured Subtracted 5791.82 6340.86 549.04
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Rooted 82.0343 78.529 3.5053
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Divided 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
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Squared Subtracted 24025.9 27585.7 3559.8
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Ranked 178.514 171.42 7.094
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 Divided 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
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Subtracted 5791.82 6340.86 549.04
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Rooted Divided 52.9804 50.0947 1.0576
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Squared Subtracted 24025.9 27585.7 3559.8
parafibromin. [refseq;acc:nm_024529] Rooted 53.2852 56.7723 3.4871
tubby protein homolog. [swissprot;acc:p50607] Ranked Divided 211.987 204.964 1.03426
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Subtracted 211.812 204.732 7.08
967 actin binding lim protein 2. [refseq;acc:nm_032432] Measured 5791.82 6340.86 549.04
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Squared 31878.5 35436.9 3558.4
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Ranked 231.277 238.356 7.079
dynactin 4. [refseq;acc:nm_032486] Rooted 55.2242 51.7372 3.487
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Squared Divided 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]
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Measured Subtracted 5791.82 6340.86 549.04
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 132.413 125.389 7.024
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Squared Divided 25580.6 29466.1 1.15189
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Ranked 211.987 204.964 1.03426
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Squared Subtracted 21890.2 25445.6 3555.4
ras-related protein rab-37. [swissprot;acc:q96ax2] Rooted 51.4945 48.0189 3.4756
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Measured Divided 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
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Ranked Subtracted 132.413 125.389 7.024

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/