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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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 [...,...].
expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 201 to 250 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.120464 0.0302145 1115 CPXM1 POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3] 0.250817672
0.120482 0.028203 1830 CASP7 CASPASE-7 PRECURSOR (EC 3.4.22.-) (ICE-LIKE APOPTOTIC PROTEASE 3) (ICE-LAP3) (APOPTOTIC PROTEASE MCH-3) (CMH-1). [SWISSPROT;Acc:P55210] 0.23408476
0.120529 0.0279282 1933 FAM98A 0.23171353
0.120575 0.0319701 707 RCOR2 0.265147004
0.120774 0.02527 2666 no value NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 0.209233775
0.120995 0.0416456 165 MSI1 MUSASHI 1. [RefSeq;Acc:NM_002442] 0.344192735
0.121057 0.0376832 257 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]" 0.311284767
0.121119 0.0337208 397 NHP2L1 NHP2-LIKE PROTEIN 1 (HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG 1) ([U4/U6.U5] TRI-SNRNP 15.5 KDA PROTEIN) (OTK27). [SWISSPROT;Acc:P55769] 0.278410489
0.12113 0.0303816 1111 CPZ CPZ GENE PRODUCT. [RefSeq;Acc:NM_003652] 0.250818129
0.121182 0.0297584 1321 TXN THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [SWISSPROT;Acc:P10599] 0.245567824
0.121383 0.0260682 2534 no value KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 0.214759892
0.121579 0.0321572 752 LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [SWISSPROT;Acc:P50851] 0.264496336
0.121992 0.0305978 1112 CPN1 CARBOXYPEPTIDASE N CATALYTIC CHAIN PRECURSOR (EC 3.4.17.3) (ARGININE CARBOXYPEPTIDASE) (KININASE 1) (SERUM CARBOXYPEPTIDASE N) (SCPN) (ANAPHYLATOXIN INACTIVATOR) (PLASMA CARBOXYPEPTIDASE B). [SWISSPROT;Acc:P15169] 0.250818086
0.122012 0.0281946 1976 POLDIP2 DNA POLYMERASE DELTA P38 SUBUNIT. [RefSeq;Acc:NM_015584] 0.231080549
0.122212 0.0258274 2612 ATP5J2 "ATP SYNTHASE F CHAIN, MITOCHONDRIAL (EC 3.6.3.14). [SWISSPROT;Acc:P56134]" 0.211332766
2613 DHX35 PROBABLE ATP-DEPENDENT HELICASE DDX35 (DEAH-BOX PROTEIN 35). [SWISSPROT;Acc:Q9H5Z1]
0.122543 0.0413389 178 no value FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333] 0.337341994
0.122604 0.0413596 176 PRMT1 PROTEIN ARGININE N-METHYLTRANSFERASE 1 (EC 2.1.1.-) (INTERFERON RECEPTOR 1-BOUND PROTEIN 4). [SWISSPROT;Acc:Q99873] 0.33734299
0.122644 0.0285481 1881 MARCH1 0.232772088
0.122661 0.030826 1097 PGAM4 PUTATIVE PHOSPHOGLYCERATE MUTASE 3 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13). [SWISSPROT;Acc:Q8N0Y7] 0.251310522
0.122715 0.0296714 1549 ARL4A ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 4. [SWISSPROT;Acc:P40617] 0.241791142
0.122748 0.034272 373 no value 0.279206179
0.122785 0.0252114 2737 VAMP2 VESICLE-ASSOCIATED MEMBRANE PROTEIN 2 (VAMP-2) (SYNAPTOBREVIN 2). [SWISSPROT;Acc:P19065] 0.205329641
2738 TMEM64
2739 VAMP4 VESICULE-ASSOCIATED MEMBRANE PROTEIN 4 (VAMP-4). [SWISSPROT;Acc:O75379]
0.12283 0.0273103 2291 TMOD2 NEURONAL TROPOMODULIN (N-TMOD) (TROPOMODULIN 2). [SWISSPROT;Acc:Q9NZR1] 0.222342262
0.123075 0.0283438 2029 SIN3A "TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [RefSeq;Acc:NM_015477]" 0.230296973
0.0305968 1189 ATP13A2 PROBABLE CATION-TRANSPORTING ATPASE 1 (EC 3.6.1.-). [SWISSPROT;Acc:Q9NQ11] 0.248602884
0.123338 0.0274232 2295 TMOD4 SKELETAL MUSCLE TROPOMODULIN (SK-TMOD) (TROPOMODULIN 4). [SWISSPROT;Acc:Q9NZQ9] 0.222341857
0.123653 0.0274568 2311 POLG DNA POLYMERASE GAMMA SUBUNIT 1 (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) (POLG-ALPHA). [SWISSPROT;Acc:P54098] 0.22204718
0.123882 0.0373888 288 PMP2 MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689] 0.301809787
0.124 0.031735 964 SSRP1 STRUCTURE-SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) (RECOMBINATION SIGNAL SEQUENCE RECOGNITION PROTEIN) (T160) (CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR 80 KDA SUBUNIT) (FACT 80 KDA SUBUNIT). [SWISSPROT;Acc:Q08945] 0.255927419
0.12412 0.0282774 2142 IRX4 IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 (IROQUOIS HOMEOBOX PROTEIN 4). [SWISSPROT;Acc:P78413] 0.227823074
2143 ZC3H12A
0.124173 0.0276089 2292 TMOD3 UBIQUITOUS TROPOMODULIN (U-TMOD) (TROPOMODULIN 3). [SWISSPROT;Acc:Q9NYL9] 0.222342216
0.124441 0.0511645 58 no value "DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 0.411154684
0.124442 0.0328701 755 CCDC93 0.264139921
0.12452 0.0375812 292 FABP4 "FATTY ACID-BINDING PROTEIN, ADIPOCYTE (AFABP) (ADIPOCYTE LIPID-BINDING PROTEIN) (ALBP) (A-FABP). [SWISSPROT;Acc:P15090]" 0.301808545
0.12454 0.0341617 493 KCMF1 "POTASSIUM CHANNEL MODULATORY FACTOR 1; POTASSIUM CHANNEL MODULATORY FACTOR; DIFFERENTIALLY EXPRESSED IN BRANCHING TUBULOGENESIS 91; ZINC FINGER, ZZ DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020122]" 0.274303035
0.124574 0.0330141 711 CAPZA3 F-ACTIN CAPPING PROTEIN ALPHA-3 SUBUNIT (CAPZ ALPHA-3) (GERM CELL- SPECIFIC PROTEIN 3). [SWISSPROT;Acc:Q96KX2] 0.265015974
0.1246 0.0303893 1421 TBL1Y "TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 0.243894864
0.125329 0.0281672 2224 MSRA PEPTIDE METHIONINE SULFOXIDE REDUCTASE (EC 1.8.4.6) (PROTEIN- METHIONINE-S-OXIDE REDUCTASE) (PEPTIDE MET(O) REDUCTASE). [SWISSPROT;Acc:Q9UJ68] 0.224746068
0.0515298 50 FTL FERRITIN LIGHT CHAIN (FERRITIN L SUBUNIT). [SWISSPROT;Acc:P02792] 0.411156237
0.125458 0.0271894 2457 ZEB2 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] 0.216721134
0.125575 0.027214 2459 C20orf80 0.21671511
0.125605 0.0306345 1420 TBL1X "TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 0.243895546
0.125634 0.0344618 490 CHCHD6 0.274303135
491 ARFGAP3 ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61]
492 no value
0.125644 0.046965 101 INPP4B "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE II, 105KD; INOSITOL POLYPHOSPHATE 4-PHOSPHATASE II; 4-PHOSPHATASE II. [RefSeq;Acc:NM_003866]" 0.373794212

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/