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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 812 to 861 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
203 TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked 201.515 228.752 1.13516
204 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured 4512.19 5655.52 1.25339
Rooted 55.8956 63.9636 1.14434
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Squared 12326.4 16522.9 1.34045
TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked 201.515 228.752 1.13516
205 LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 200.968 1.13501
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured 4512.19 5655.52 1.25339
Rooted 55.8956 63.9636 1.14434
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Squared 12326.4 16522.9 1.34045
206 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured 5720.25 4577.5 1.24965
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted 140.508 122.878 1.14348
DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Squared 12326.4 16522.9 1.34045
LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 228.085 201.006 1.13472
207 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Measured 4771.21 5961.43 1.24946
ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Rooted 140.508 122.878 1.14348
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked 285.684 252.234 1.13261
SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Squared 70525.9 52678.7 1.33879
208 CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Measured 4068.78 5082.18 1.24907
CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Squared 70525.9 52678.7 1.33879
DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Rooted 46.901 53.624 1.14334
SKP1A 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] Ranked 285.684 252.234 1.13261
209 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Measured 4068.78 5082.18 1.24907
CAPN2 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] Rooted 46.8525 53.5324 1.14257
CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Squared 70525.9 52678.7 1.33879
FBXW7 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] Ranked 285.684 252.234 1.13261
210 CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Measured 4068.82 5082.21 1.24906
CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted 46.8525 53.5316 1.14256
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked 285.684 252.234 1.13261
SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared 69549 92953.5 1.33652
211 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Measured 4068.91 5082.27 1.24905
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Rooted 88.4361 77.5112 1.14095
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 252.234 1.13261
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Squared 14668.3 19547 1.3326
212 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted 88.4266 77.5047 1.14092
BRF1 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] Measured 4446.72 5553.79 1.24896
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 252.234 1.13261
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Squared 14690.3 19560.2 1.3315
213 NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Measured 4446.72 5553.79 1.24896
PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Ranked 210.693 186.95 1.127
STAM signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared 86861.5 65369.7 1.32877
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted 105.205 92.2415 1.14054
214 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 4074.83 5086.49 1.24827
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted 105.205 92.2415 1.14054
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked 191.644 170.192 1.12605
TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared 52591.3 69845.1 1.32807
215 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked 112 126 1.125
KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured 16074 12888.4 1.24717
PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared 86609.4 65234.5 1.32766
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 92.2415 1.14054
216 MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Ranked 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/