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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 873 to 922 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
Value Type
description
red
network_comparison
green
110 Divided CACNG4 Rooted voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 49.293 1.26585 62.3973
DTX2 Ranked deltex 2. [refseq;acc:nm_020892] 333.144 1.2459 267.393
MYH8 Squared myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 19321 1.54043 12542.6
PRMT1 Measured protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 4366.44 1.35116 5899.76
Subtracted no value Squared pnas-18. [sptrembl;acc:q9bzu3] 87787.3 29631.5 58155.8
JPH3 Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 33.9632 15.5377 18.4255
NAPG Ranked gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 39.888 249.187
PPP1R8 Measured nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 17385.9 2496.7 14889.2
111 Divided CACNG3 Rooted voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 49.2923 1.26585 62.3969
DTX1 Ranked deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 332.925 1.24563 267.274
MYH2 Squared myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 19321 1.54043 12542.6
PRMT8 Measured protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 4366.44 1.35116 5899.76
Subtracted ACADVL Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 79779.8 28304.2 108084
CCT3 Measured t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 12365.2 2459.7 14824.9
GAD1 Ranked glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 209.299 39.888 249.187
JPH2 Rooted junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 33.9632 15.5377 18.4255
112 Divided CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 49.3267 1.26537 62.4167
MYH3 Squared myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 19321 1.54043 12542.6
PBK Ranked t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 332.874 1.24557 267.246
SNRP70 Measured u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 4366.44 1.35116 5899.76
Subtracted ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 2405.69 9352.11
CTPS2 Squared cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 96730.5 27443.8 69286.7
POLE4 Ranked dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 275.754 39.846 235.908
SMPD2 Rooted sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 33.9632 15.5377 18.4255
113 Divided no value Measured filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 4366.44 1.35116 5899.76
ARRB2 Rooted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 80.4705 1.26165 101.526
KHDRBS3 Ranked kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 332.874 1.24557 267.246
MYH1 Squared myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 19321 1.54043 12542.6
Subtracted ATF3 Measured cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 2331.9 7132.71
CTPS Squared ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 96602.7 27391.5 69211.2
PPP2CA Ranked serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 194.372 39.832 234.204
TMEM33 Rooted db83 protein. [swissprot;acc:p57088] 33.9632 15.5377 18.4255
114 Divided no value Squared myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 19321 1.54043 12542.6
ARRB1 Rooted beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 80.4705 1.26165 101.526
KHDRBS1 Ranked kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 332.874 1.24557 267.246
PRPF40B Measured huntingtin interacting protein c. [refseq;acc:nm_012272] 4300.47 1.35048 5807.72
Subtracted no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 13768.2 2302.2 11466
ATG12 Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 67438.6 26741.6 40697
B9D1 Ranked b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 37.447 267.265
GNB5 Rooted guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 40.225 15.5199 24.7051
115 Divided KHDRBS2 Ranked kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 332.874 1.24557 267.246
MRPS17 Measured 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 21185 1.34491 28492
MYH7B Squared dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 19321 1.54043 12542.6
SPATA6 Rooted spermatogenesis associated 6. [refseq;acc:nm_019073] 80.4705 1.26165 101.526
Subtracted no value Measured pnas-18. [sptrembl;acc:q9bzu3] 13680.5 2270.9 11409.6
Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 72886.3 25658.2 98544.5
DGCR14 Rooted dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 21.4476 15.4983 36.9459
HAT1 Ranked histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 277.546 37.085 240.461
116 Divided AMPD2 Rooted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 80.4705 1.26165 101.526
GNB3 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 268.565 1.24545 334.483

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/