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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 833 to 882 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
209 CACNG3 Measured voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 4068.78 5082.18 1.24907
CAPN2 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
CTNNAL1 Squared catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 70525.9 52678.7 1.33879
FBXW7 Ranked 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] 285.684 252.234 1.13261
210 CACNG2 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
CAPN1 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
CUL2 Ranked cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 252.234 1.13261
SGTA Squared small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 69549 92953.5 1.33652
211 CACNG4 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
PITRM1 Rooted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 88.4361 77.5112 1.14095
PSEN1 Ranked presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 285.684 252.234 1.13261
TIA1 Squared nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 14668.3 19547 1.3326
212 ALG1 Rooted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 88.4266 77.5047 1.14092
BRF1 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
CUL1 Ranked cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 1.13261
TIAL1 Squared nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 14690.3 19560.2 1.3315
213 NOLA1 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1.24896
PLDN Ranked pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127
STAM Squared signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] 86861.5 65369.7 1.32877
STAMBPL1 Rooted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 105.205 92.2415 1.14054
214 CACNG5 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
CHMP2A Rooted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 105.205 92.2415 1.14054
LASS2 Ranked lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
TRMU Squared trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 52591.3 69845.1 1.32807
215 no value Ranked myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 112 126 1.125
KRAS Measured transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 16074 12888.4 1.24717
PRKCH Squared protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] 86609.4 65234.5 1.32766
STAMBP Rooted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 105.205 92.2415 1.14054
216 MYH4 Ranked myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 112 126 1.125
PRKCE Squared protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 86600.9 65229.9 1.32763
SHOC2 Measured leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 16071.6 12886.8 1.24714
VPS24 Rooted neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 105.205 92.2415 1.14054
217 no value Measured ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 16071.6 12886.8 1.24714
CHMP4A Rooted protein hspc134 (protein cda04). [swissprot;acc:q9by43] 105.205 92.2415 1.14054
MYH8 Ranked myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 112 126 1.125
PPIB 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
218 no value Rooted hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 46.1476 52.5742 1.13926
HRAS Measured transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 16070.4 12886 1.24712
MYH2 Ranked myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 112 126 1.125
OGT 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
219 no value Measured transforming protein n-ras. [swissprot;acc:p01111] 16069.8 12885.6 1.24711
COX4I1 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
MYH3 Ranked myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 112 126 1.125
RBBP7 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 no value 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
COX4I2 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
MTA1 Rooted metastasis-associated protein mta1. [swissprot;acc:q13330] 52.7557 60.035 1.13798
MYH1 Ranked myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 112 126 1.125
221 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
HPRT1 Squared hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 70739 93908.8 1.32754

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/