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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 382 to 431 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
191 Subtracted no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 25.979 241.373 267.352
192 Divided MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] 1.14055 227.491 199.458
Subtracted LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 25.979 241.373 267.352
193 Divided MSI1 musashi 1. [refseq;acc:nm_002442] 1.14055 227.491 199.458
Subtracted PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 25.979 241.373 267.352
194 Divided ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] 1.14055 227.491 199.458
Subtracted POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 25.979 241.373 267.352
195 Divided PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] 1.13748 227.971 200.417
Subtracted PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 25.979 241.373 267.352
196 Divided FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1.13745 263.215 231.407
Subtracted no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 25.889 272.781 246.892
197 Divided FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 1.13745 263.215 231.407
Subtracted SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] 25.839 241.13 266.969
198 Divided FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 1.13741 263.191 231.394
Subtracted no value 40s ribosomal protein s29. [swissprot;acc:p30054] 25.793 241.849 267.642
199 Divided EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 1.13729 242.735 276.059
Subtracted RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] 25.689 241.399 267.088
200 Divided EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 1.1372 242.718 276.018
Subtracted no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 25.527 241.808 267.335
201 Divided SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1.13601 240.133 211.382
Subtracted RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 25.518 241.828 267.346
202 Divided TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1.13553 201.478 228.784
Subtracted RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 25.321 240.758 266.079
203 Divided TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 1.13516 201.515 228.752
Subtracted no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 25.32 240.758 266.078
204 Divided TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 1.13516 201.515 228.752
Subtracted 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] 25.044 268.632 243.588
205 Divided LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1.13501 228.1 200.968
Subtracted CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 25.043 268.635 243.592
206 Divided LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1.13472 228.085 201.006
Subtracted RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] 25.003 241.411 266.414
207 Divided PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 1.13261 285.684 252.234
Subtracted EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 24.949 237.312 212.363
208 Divided 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] 1.13261 285.684 252.234
Subtracted no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 24.935 240.782 265.717
209 Divided 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] 1.13261 285.684 252.234
Subtracted BCCIP 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] 24.935 240.782 265.717
210 Divided CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1.13261 285.684 252.234
Subtracted no value rna-binding protein. [refseq;acc:nm_019027] 24.892 237.302 212.41
211 Divided PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1.13261 285.684 252.234
Subtracted no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 24.892 237.302 212.41
212 Divided CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1.13261 285.684 252.234
Subtracted SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] 24.892 237.302 212.41
213 Divided PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 1.127 210.693 186.95
Subtracted HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 24.892 237.302 212.41
214 Divided LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1.12605 191.644 170.192
Subtracted MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 24.838 241.282 266.12
215 Divided no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 1.125 112 126
Subtracted EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 24.835 237.292 212.457
216 Divided MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 1.125 112 126

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/