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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 836 to 885 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
209 Rooted calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 46.8525 53.5324 1.14257
210 Measured voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 4068.82 5082.21 1.24906
Ranked cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 252.234 1.13261
Squared small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 69549 92953.5 1.33652
Rooted calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 46.8525 53.5316 1.14256
211 Measured voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 4068.91 5082.27 1.24905
Ranked presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 285.684 252.234 1.13261
Squared nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 14668.3 19547 1.3326
Rooted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 88.4361 77.5112 1.14095
212 Measured transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 4446.72 5553.79 1.24896
Ranked cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 1.13261
Squared nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 14690.3 19560.2 1.3315
Rooted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 88.4266 77.5047 1.14092
213 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1.24896
Ranked pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127
Squared signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] 86861.5 65369.7 1.32877
Rooted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 105.205 92.2415 1.14054
214 Measured voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 4074.83 5086.49 1.24827
Ranked lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
Squared trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 52591.3 69845.1 1.32807
Rooted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 105.205 92.2415 1.14054
215 Measured transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 16074 12888.4 1.24717
Ranked myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 112 126 1.125
Squared protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] 86609.4 65234.5 1.32766
Rooted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 105.205 92.2415 1.14054
216 Measured leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 16071.6 12886.8 1.24714
Ranked myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 112 126 1.125
Squared protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 86600.9 65229.9 1.32763
Rooted neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 105.205 92.2415 1.14054
217 Measured ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 16071.6 12886.8 1.24714
Ranked myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 112 126 1.125
Squared peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 86600.9 65229.9 1.32763
Rooted protein hspc134 (protein cda04). [swissprot;acc:q9by43] 105.205 92.2415 1.14054
218 Measured transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 16070.4 12886 1.24712
Ranked myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 112 126 1.125
Squared udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] 86600.9 65229.9 1.32763
Rooted hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 46.1476 52.5742 1.13926
219 Measured transforming protein n-ras. [swissprot;acc:p01111] 16069.8 12885.6 1.24711
Ranked myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 112 126 1.125
Squared 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] 86600.9 65229.9 1.32763
Rooted histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 52.7146 60.0088 1.13837
220 Measured 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] 41482.5 33356.5 1.24361
Ranked myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 112 126 1.125
Squared cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 86600.9 65229.9 1.32763
Rooted metastasis-associated protein mta1. [swissprot;acc:q13330] 52.7557 60.035 1.13798
221 Measured cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 33356.5 1.24361
Ranked myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 112 126 1.125
Squared hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 70739 93908.8 1.32754
Rooted spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 56.9506 64.7888 1.13763
222 Measured cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 33356.5 1.24361

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/