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 [...,...].
measured Rank Gene description expected final Hugo
Results: HTML CSV LaTeX Showing element 401 to 450 of 3206 in total
measured
Rank
description
expected
final
Hugo
0.0337015 2462 FRG1 PROTEIN (FSHD REGION GENE 1 PROTEIN). [SWISSPROT;Acc:Q14331] 0.155511 0.216714573 FRG1
2463 TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [RefSeq;Acc:NM_006354] TADA3L
0.0337208 397 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] 0.121119 0.278410489 NHP2L1
0.0337232 1599 IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [SWISSPROT;Acc:P78318] 0.140465 0.240082583 IGBP1
0.0337699 949 "OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [SWISSPROT;Acc:Q9Y3B8]" 0.131705 0.256405603 REXO2
0.0337842 1494 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1 (BREFELDIN A-INHIBITED GEP 1) (P200 ARF-GEP1) (P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR). [SWISSPROT;Acc:Q9Y6D6] 0.139157 0.242777582 ARFGEF1
0.0338352 1518 SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS-1) (JAK-BINDING PROTEIN) (JAB) (STAT INDUCED STAT INHIBITOR 1) (SSI-1) (TEC-INTERACTING PROTEIN 3) (TIP-3). [SWISSPROT;Acc:O15524] 0.13962 0.242337774 SOCS1
1519 FK506-BINDING PROTEIN 1A (EC 5.2.1.8) (PEPTIDYL-PROLYL CIS-TRANS ISOMERASE) (PPIASE) (ROTAMASE) (12 KDA FKBP) (FKBP-12) (IMMUNOPHILIN FKBP12). [SWISSPROT;Acc:P20071] FKBP1A
0.0338955 1699 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] 0.142498 0.237866496 ASNSD1
0.0339667 1259 0.137332 0.247332741 AQR
0.0340138 1650 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" 0.142333 0.238973393 CABC1
1651 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] ADCK1
1652 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853] ADCK2
0.0340698 1104 "U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B"". [SWISSPROT;Acc:P08579]" 0.135722 0.251026363 SNRPB2
0.0341617 493 "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]" 0.12454 0.274303035 KCMF1
0.0341846 592 "SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [SWISSPROT;Acc:O15020]" 0.126926 0.269327009 SPTBN2
0.0341996 1874 CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021] 0.146922 0.232773853 MARCH8
0.0342505 2124 T-COMPLEX 11. [RefSeq;Acc:NM_018679] 0.150141 0.228122232 TCP11
0.034272 373 0.122748 0.279206179 no value
0.034279 1378 GLYCOGEN SYNTHASE KINASE-3 BETA (EC 2.7.1.37) (GSK-3 BETA). [SWISSPROT;Acc:P49841] 0.140116 0.244647292 GSK3B
0.0342868 1072 IMPORTIN-ALPHA RE-EXPORTER (CHROMOSOME SEGREGATION 1-LIKE PROTEIN) (CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN). [SWISSPROT;Acc:P55060] 0.135906 0.252283196 CSE1L
0.0342893 1272 I-KAPPA-B-INTERACTING RAS-LIKE PROTEIN 2. [RefSeq;Acc:NM_017595] 0.139064 0.246572082 NKIRAS2
0.0343037 2511 0.159725 0.214767256 C20orf42
0.0343914 2154 Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24] 0.151289 0.227322542 TMBIM4
0.0344025 2358 PROTOCADHERIN 15 PRECURSOR. [SWISSPROT;Acc:Q96QU1] 0.156164 0.220297252 PCDH15
0.0344093 831 "MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 4.1.1.9) (MCD). [SWISSPROT;Acc:O95822]" 0.131824 0.261024548 MLYCD
0.0344183 1054 PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 0.136218 0.252670719 PDCL
1055 DNA REPAIR PROTEIN RAD52 HOMOLOG. [SWISSPROT;Acc:P43351] RAD52
0.0344618 490 0.125634 0.274303135 CHCHD6
491 ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61] ARFGAP3
492 no value
0.0345092 881 "PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [RefSeq;Acc:NM_002645]" 0.132688 0.260077776 PIK3C2A
0.0346049 2436 0.159272 0.2172692 SETD3
0.0348108 931 SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547] 0.135208 0.257461097 SCOC
0.0349396 1078 0.138505 0.252262373 UBE2W
0.0349473 987 ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375] 0.136958 0.255168008 ABT1
0.0349547 912 0.135465 0.258034917 SLC37A2
0.0349958 1338 SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691] 0.142675 0.245283336 SRPK2
0.0350787 2174 SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680] 0.154573 0.226939375 SCYL1
2175 TATA ELEMENT MODULATORY FACTOR (TMF). [SWISSPROT;Acc:P82094] TMF1
2176 MRNA-ASSOCIATED PROTEIN MRNP 41 (RAE1 PROTEIN HOMOLOG). [SWISSPROT;Acc:P78406] RAE1
2177 AMMECR1 PROTEIN. [RefSeq;Acc:NM_015365] AMMECR1
0.035086 1690 SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6] 0.147362 0.238093946 NEK1
0.0355659 276 ENTEROPEPTIDASE PRECURSOR (EC 3.4.21.9) (ENTEROKINASE). [SWISSPROT;Acc:P98073] 0.116699 0.304766108 PRSS7
0.0355674 767 0.134909 0.263639935 RAB11FIP2
0.035571 2979 HOMEOBOX PROTEIN HOX-B5 (HOX-2A) (HHO.C10) (HU-1). [SWISSPROT;Acc:P09067] 0.254881 0.139559245 HOXB5
0.0356563 1049 CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967] 0.14106 0.252773997 CLGN
0.035822 660 SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138] 0.134108 0.267113073 SMOC2
0.0358609 540 0.13229 0.271077935 LRRC4B
0.0359383 2654 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828] 0.171181 0.209943276 SCAMP3

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/