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 description Network Comparison Type Hugo Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 832 to 881 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Hugo
Interaction Map
red
green
network_comparison
208 s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Divided SKP1A High confidence 285.684 252.234 1.13261
209 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted BCCIP 240.782 265.717 24.935
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Divided FMO3 Low confidence 209.778 199.757 1.05017
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] FBXW7 High confidence 285.684 252.234 1.13261
jm1 protein. [refseq;acc:nm_014008] Subtracted CCDC22 Low confidence 216.308 206.292 10.016
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Divided CUL2 High confidence 285.684 252.234 1.13261
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Subtracted FMO1 Low confidence 209.768 199.756 10.012
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Divided FMO2 209.782 199.761 1.05016
rna-binding protein. [refseq;acc:nm_019027] Subtracted no value High confidence 237.302 212.41 24.892
211 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Divided FMO1 Low confidence 209.768 199.756 1.05012
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Subtracted FMO4 209.765 199.755 10.01
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided PSEN1 High confidence 285.684 252.234 1.13261
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Low confidence 211.383 221.976 1.05011
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted SYNCRIP High confidence 237.302 212.41 24.892
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Low confidence 201.43 191.43 10
213 a kindred of iglon. [refseq;acc:nm_173808] NEGR1 199.671 209.654 9.983
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Divided FMO4 209.765 199.755 1.05011
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Subtracted HNRNPR High confidence 237.302 212.41 24.892
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided PLDN 210.693 186.95 1.127
214 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 191.644 170.192 1.12605
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Subtracted MRPL4 241.282 266.12 24.838
neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336] NMBR Low confidence 199.671 209.654 9.983
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Divided OGT 206.583 196.743 1.05001
215 a kindred of iglon. [refseq;acc:nm_173808] NEGR1 199.671 209.654 1.05
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Subtracted EIF4G1 High confidence 237.292 212.457 24.835
gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [swissprot;acc:p30550] GRPR Low confidence 199.671 209.654 9.983
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided no value High confidence 112 126 1.125
216 bombesin receptor subtype-3 (brs-3). [swissprot;acc:p32247] Subtracted BRS3 Low confidence 199.671 209.654 9.983
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Divided MYH4 High confidence 112 126 1.125
neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336] NMBR Low confidence 199.671 209.654 1.05
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted SNRPD2 High confidence 226.471 201.769 24.702
217 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 242.326 267.008 24.682
gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [swissprot;acc:p30550] Divided GRPR Low confidence 199.671 209.654 1.05
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 High confidence 112 126 1.125
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Subtracted OGT Low confidence 206.583 196.743 9.84
218 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 High confidence 242.333 266.999 24.666
bombesin receptor subtype-3 (brs-3). [swissprot;acc:p32247] Divided BRS3 Low confidence 199.671 209.654 1.05
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Subtracted LEF1 208.289 198.538 9.751
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided MYH2 High confidence 112 126 1.125
219 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted no value 242.339 266.986 24.647
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] NFYA Low confidence 214.032 204.284 9.748
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided MYH3 High confidence 112 126 1.125
transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] BACH1 Low confidence 172.647 164.44 1.04991
220 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Subtracted MRPL2 High confidence 242.339 266.986 24.647
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided MYH1 112 126 1.125
nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 Low confidence 172.647 164.44 1.04991
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Subtracted TLR2 207.926 198.276 9.65
221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Divided no value High confidence 112 126 1.125

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/